Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/inputs/xbz Working: n-5-33.cluster.ucsf.bkslab.org:/scratch/xiaobo/316102/xbz-8058115.52 Result: /scratch/xiaobo/316102/xbz-8058115.52 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbz Task: /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent --pre-tautomerized --permissive-taut-prot /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/inputs/xbz mkdir: created directory `/scratch/xiaobo/316102' mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52' /scratch/xiaobo/316102/xbz-8058115.52 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/logs NOTICE: Using permissive tautomer and protomer thresholds. Could produce many protomers! STORE_PROTOMERS is not set! Will keep all results to finished directory mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working' mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/protonate' Storing results in /scratch/xiaobo/316102/xbz-8058115.52/finished Working in /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 /scratch/xiaobo/316102/xbz-8058115.52/working/protonate /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Using inputs as protomers/tautomers. No processing done 455 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/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Bulk generating 3D conformations all protomers in /scratch/xiaobo/316102/xbz-8058115.52/working/3D mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/316102/xbz-8058115.52/working/protonate/xbz-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 ZINC001467729094 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building' mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC001467729094 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/1 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN(C)CCN(CC)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001467729094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467729094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001467729094 none C=CCN(C)CCN(CC)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 10, 5, 3, 2, 3, 4, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 16, 16, 16, 16, 10, 10, 10, 5, 5, 5, 5, 4, 4, 4, 4, 4, 2, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/2 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN(C)CCN(CC)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001467729094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467729094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001467729094 none C=CCN(C)CCN(CC)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 12, 6, 4, 2, 4, 5, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 19, 19, 19, 18, 18, 12, 12, 12, 6, 6, 6, 6, 5, 5, 5, 5, 5, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [45, 41, 10, 46, 12, 13, 14, 15, 16, 17, 21, 22, 23, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 98 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/3 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/3' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN(C)CCN(CC)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001467729094.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001467729094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001467729094 none C=CCN(C)CCN(CC)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 12, 6, 4, 2, 4, 5, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 19, 19, 19, 18, 18, 12, 12, 12, 6, 6, 6, 6, 5, 5, 5, 5, 5, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [45, 41, 10, 46, 12, 13, 14, 15, 16, 17, 21, 22, 23, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 98 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001467729094 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/finished' Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/2.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 Building ZINC001467729094 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC001467729094 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 1) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN(C)CCN(CC)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001467729094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467729094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001467729094 none C=CCN(C)CCN(CC)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 10, 5, 3, 2, 3, 4, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 16, 16, 16, 16, 10, 10, 10, 5, 5, 5, 5, 4, 4, 4, 4, 4, 2, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 2) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN(C)CCN(CC)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001467729094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467729094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001467729094 none C=CCN(C)CCN(CC)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 12, 6, 4, 2, 4, 5, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 19, 19, 19, 18, 18, 12, 12, 12, 6, 6, 6, 6, 5, 5, 5, 5, 5, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [45, 41, 10, 46, 12, 13, 14, 15, 16, 17, 21, 22, 23, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 98 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 3) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN(C)CCN(CC)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001467729094.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001467729094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001467729094 none C=CCN(C)CCN(CC)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 12, 6, 4, 2, 4, 5, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 19, 19, 19, 18, 18, 12, 12, 12, 6, 6, 6, 6, 5, 5, 5, 5, 5, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [45, 41, 10, 46, 12, 13, 14, 15, 16, 17, 21, 22, 23, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 98 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001467729094 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/2.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 Building ZINC001467729094 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC001467729094 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 1) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN(C)CCN(CC)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001467729094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467729094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001467729094 none C=CCN(C)CCN(CC)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 10, 5, 3, 2, 3, 4, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 16, 16, 16, 16, 10, 10, 10, 5, 5, 5, 5, 4, 4, 4, 4, 4, 2, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 2) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN(C)CCN(CC)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001467729094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467729094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001467729094 none C=CCN(C)CCN(CC)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 12, 6, 4, 2, 4, 5, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 19, 19, 19, 18, 18, 12, 12, 12, 6, 6, 6, 6, 5, 5, 5, 5, 5, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [45, 41, 10, 46, 12, 13, 14, 15, 16, 17, 21, 22, 23, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 98 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 3) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN(C)CCN(CC)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001467729094.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001467729094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001467729094 none C=CCN(C)CCN(CC)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 12, 6, 4, 2, 4, 5, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 19, 19, 19, 18, 18, 12, 12, 12, 6, 6, 6, 6, 5, 5, 5, 5, 5, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [45, 41, 10, 46, 12, 13, 14, 15, 16, 17, 21, 22, 23, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 98 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001467729094 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/2.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001467729094 Building ZINC001472034158 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001472034158 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/4 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1) `ZINC001472034158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/5 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1) `ZINC001472034158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/6 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/6' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1) `ZINC001472034158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/7 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/7' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1) `ZINC001472034158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001472034158 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 Building ZINC001472034158 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001472034158 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 4) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1) `ZINC001472034158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 5) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1) `ZINC001472034158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 6) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1) `ZINC001472034158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 7) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1) `ZINC001472034158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001472034158 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 Building ZINC001472034158 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001472034158 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 4) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1) `ZINC001472034158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 5) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1) `ZINC001472034158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 6) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1) `ZINC001472034158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 7) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1) `ZINC001472034158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001472034158 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 Building ZINC001472034158 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001472034158 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 4) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1) `ZINC001472034158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 5) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1) `ZINC001472034158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 6) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1) `ZINC001472034158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 7) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1) `ZINC001472034158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001472034158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001472034158 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001472034158 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001472034158 Building ZINC001512908835 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512908835 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/8 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001512908835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512908835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001512908835 none C=CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 44, 20, 20, 20, 8, 6, 8, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 20, 20, 50, 50, 50, 50, 50, 44, 44, 20, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/9 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001512908835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512908835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001512908835 none C=CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 20, 20, 20, 10, 7, 10, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 20, 20, 50, 50, 50, 50, 50, 42, 42, 20, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001512908835 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835 Building ZINC001512908835 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512908835 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 8) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001512908835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512908835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001512908835 none C=CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 44, 20, 20, 20, 8, 6, 8, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 20, 20, 50, 50, 50, 50, 50, 44, 44, 20, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 9) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001512908835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512908835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001512908835 none C=CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 20, 20, 20, 10, 7, 10, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 20, 20, 50, 50, 50, 50, 50, 42, 42, 20, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001512908835 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001512908835 Building ZINC001513351477 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513351477 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/10 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001513351477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513351477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513351477 none C#CCNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 47, 28, 47, 10, 7, 10, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 8, 7, 50, 50, 50, 47, 28, 28, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/11 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001513351477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513351477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513351477 none C#CCNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 47, 29, 47, 8, 6, 8, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 6, 50, 50, 50, 47, 29, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001513351477 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477 Building ZINC001513351477 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513351477 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 10) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001513351477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513351477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513351477 none C#CCNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 47, 28, 47, 10, 7, 10, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 8, 7, 50, 50, 50, 47, 28, 28, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 11) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001513351477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513351477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513351477 none C#CCNC(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 47, 29, 47, 8, 6, 8, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 6, 50, 50, 50, 47, 29, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001513351477 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513351477 Building ZINC001513477747 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001513477747 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/12 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 10, 26, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 26, 50, 50, 50, 26, 26, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 26, 26, 26, 26] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/13 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 25, 25, 25, 25, 8, 25, 6, 8, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 50, 50, 50, 25, 25, 25, 25, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 25, 25, 25, 25] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/14 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/14' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 10, 26, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 26, 50, 50, 50, 26, 26, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 26, 26, 26, 26] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/15 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/15' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 8, 26, 6, 8, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 26, 26, 50, 50, 50, 26, 26, 26, 26, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 26, 26, 26, 26] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001513477747 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 Building ZINC001513477747 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001513477747 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 12) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 10, 26, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 26, 50, 50, 50, 26, 26, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 26, 26, 26, 26] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 13) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 25, 25, 25, 25, 8, 25, 6, 8, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 50, 50, 50, 25, 25, 25, 25, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 25, 25, 25, 25] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 14) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 10, 26, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 26, 50, 50, 50, 26, 26, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 26, 26, 26, 26] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 15) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 8, 26, 6, 8, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 26, 26, 50, 50, 50, 26, 26, 26, 26, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 26, 26, 26, 26] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001513477747 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 Building ZINC001513477747 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001513477747 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 12) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 10, 26, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 26, 50, 50, 50, 26, 26, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 26, 26, 26, 26] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 13) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 25, 25, 25, 25, 8, 25, 6, 8, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 50, 50, 50, 25, 25, 25, 25, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 25, 25, 25, 25] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 14) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 10, 26, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 26, 50, 50, 50, 26, 26, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 26, 26, 26, 26] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 15) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 8, 26, 6, 8, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 26, 26, 50, 50, 50, 26, 26, 26, 26, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 26, 26, 26, 26] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001513477747 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 Building ZINC001513477747 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001513477747 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 12) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 10, 26, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 26, 50, 50, 50, 26, 26, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 26, 26, 26, 26] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 13) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 25, 25, 25, 25, 8, 25, 6, 8, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 50, 50, 50, 25, 25, 25, 25, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 25, 25, 25, 25] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 14) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 10, 26, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 26, 50, 50, 50, 26, 26, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 26, 26, 26, 26] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 15) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001513477747.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001513477747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477747 none C#CC[N@]1CC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 8, 26, 6, 8, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 26, 26, 50, 50, 50, 26, 26, 26, 26, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 26, 26, 26, 26] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001513477747 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001513477747 Building ZINC001539118769 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001539118769 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/16 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/16' -> `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)N1C[C@H]2CS(=O)(=O)C[C@@]2(C#N)C1) `ZINC001539118769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001539118769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001539118769 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CS(=O)(=O)C[C@@]2(C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 11, 11, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 3, 3, 3, 3, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 49 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/17 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/17' -> `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)N1C[C@H]2CS(=O)(=O)C[C@@]2(C#N)C1) `ZINC001539118769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001539118769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001539118769 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CS(=O)(=O)C[C@@]2(C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 11, 11, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 3, 3, 3, 3, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 49 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001539118769 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769 Building ZINC001539118769 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001539118769 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 16) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CS(=O)(=O)C[C@@]2(C#N)C1) `ZINC001539118769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001539118769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001539118769 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CS(=O)(=O)C[C@@]2(C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 11, 11, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 3, 3, 3, 3, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 49 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 17) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CS(=O)(=O)C[C@@]2(C#N)C1) `ZINC001539118769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001539118769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001539118769 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CS(=O)(=O)C[C@@]2(C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 11, 11, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 3, 3, 3, 3, 3, 3, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 49 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001539118769 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539118769 Building ZINC001542487490 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542487490 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/18 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(Br)CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001542487490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542487490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001542487490 none C=C(Br)CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'Br', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 17, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 25, 25, 14, 14, 3, 2, 5, 5, 2, 2, 2, 2] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/19 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(Br)CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001542487490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542487490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001542487490 none C=C(Br)CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'Br', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 17, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 25, 25, 14, 14, 3, 2, 5, 5, 2, 2, 2, 2] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001542487490 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490 Building ZINC001542487490 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542487490 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 18) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(Br)CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001542487490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542487490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001542487490 none C=C(Br)CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'Br', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 17, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 25, 25, 14, 14, 3, 2, 5, 5, 2, 2, 2, 2] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 19) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(Br)CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001542487490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542487490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001542487490 none C=C(Br)CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'Br', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 17, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 25, 25, 14, 14, 3, 2, 5, 5, 2, 2, 2, 2] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001542487490 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001542487490 Building ZINC001565815669 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001565815669 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/20 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 18, 18, 18, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/21 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 17, 17, 17, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/22 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/22' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 18, 18, 18, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/23 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/23' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 17, 17, 17, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001565815669 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 Building ZINC001565815669 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001565815669 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 20) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 18, 18, 18, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 21) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 17, 17, 17, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 22) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 18, 18, 18, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 23) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 17, 17, 17, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001565815669 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 Building ZINC001565815669 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001565815669 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 20) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 18, 18, 18, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 21) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 17, 17, 17, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 22) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 18, 18, 18, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 23) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 17, 17, 17, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001565815669 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 Building ZINC001565815669 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001565815669 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 20) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 18, 18, 18, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 21) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 17, 17, 17, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 22) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 18, 18, 18, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 23) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001565815669.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001565815669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001565815669 none C#CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 17, 17, 17, 9, 9, 9, 9, 9, 9, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [33, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001565815669 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565815669 Building ZINC001565945317 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565945317 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/24 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNCC(=O)NCC#N) `ZINC001565945317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565945317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001565945317 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNCC(=O)NCC#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 22, 39, 41, 41, 41, 50, 50, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 22, 39, 39, 41, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/25 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNCC(=O)NCC#N) `ZINC001565945317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565945317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001565945317 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNCC(=O)NCC#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 16, 25, 38, 41, 41, 41, 50, 50, 6, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 25, 38, 38, 41, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001565945317 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317 Building ZINC001565945317 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565945317 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 24) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNCC(=O)NCC#N) `ZINC001565945317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565945317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001565945317 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNCC(=O)NCC#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 22, 39, 41, 41, 41, 50, 50, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 22, 39, 39, 41, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 25) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNCC(=O)NCC#N) `ZINC001565945317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565945317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001565945317 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNCC(=O)NCC#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 16, 25, 38, 41, 41, 41, 50, 50, 6, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 25, 38, 38, 41, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001565945317 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001565945317 Building ZINC001626913232 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626913232 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/26 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cn1cnnn1)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001626913232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626913232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001626913232 none O=C(Cn1cnnn1)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 16, 28, 36, 36, 36, 36, 11, 11, 11, 5, 2, 6, 1, 1, 1, 3, 3, 5, 5, 3, 3, 5, 5, 11, 11, 28, 28, 36, 11, 11, 11, 11, 3, 3, 5, 5, 5, 5, 11, 11, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/27 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cn1cnnn1)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001626913232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626913232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001626913232 none O=C(Cn1cnnn1)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 32, 32, 32, 32, 12, 12, 12, 6, 1, 8, 1, 1, 1, 3, 3, 5, 5, 3, 3, 5, 5, 12, 12, 23, 23, 32, 12, 12, 12, 12, 3, 3, 5, 5, 5, 5, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 107 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001626913232 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232 Building ZINC001626913232 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626913232 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 26) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(Cn1cnnn1)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001626913232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626913232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001626913232 none O=C(Cn1cnnn1)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 16, 28, 36, 36, 36, 36, 11, 11, 11, 5, 2, 6, 1, 1, 1, 3, 3, 5, 5, 3, 3, 5, 5, 11, 11, 28, 28, 36, 11, 11, 11, 11, 3, 3, 5, 5, 5, 5, 11, 11, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 27) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(Cn1cnnn1)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001626913232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626913232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001626913232 none O=C(Cn1cnnn1)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 32, 32, 32, 32, 12, 12, 12, 6, 1, 8, 1, 1, 1, 3, 3, 5, 5, 3, 3, 5, 5, 12, 12, 23, 23, 32, 12, 12, 12, 12, 3, 3, 5, 5, 5, 5, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 107 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001626913232 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001626913232 Building ZINC001635631281 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635631281 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/28 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001635631281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635631281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001635631281 none C=C(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens 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, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 2, 1, 4, 4, 1, 1, 1, 1, 14, 14, 14] 50 rigid atoms, others: [33, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 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/316102/xbz-8058115.52/working/building/ZINC001635631281 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/29 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001635631281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635631281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001635631281 none C=C(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens 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, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 4, 4, 1, 1, 1, 1, 15, 15, 15] 50 rigid atoms, others: [33, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 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/316102/xbz-8058115.52/working/building/ZINC001635631281 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001635631281 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281 Building ZINC001635631281 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635631281 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 28) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001635631281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635631281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001635631281 none C=C(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens 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, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 2, 1, 4, 4, 1, 1, 1, 1, 14, 14, 14] 50 rigid atoms, others: [33, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 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/316102/xbz-8058115.52/working/building/ZINC001635631281 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 29) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001635631281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635631281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001635631281 none C=C(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens 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, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 4, 4, 1, 1, 1, 1, 15, 15, 15] 50 rigid atoms, others: [33, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 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/316102/xbz-8058115.52/working/building/ZINC001635631281 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001635631281 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631281 Building ZINC001635631282 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635631282 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/30 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001635631282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635631282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001635631282 none C=C(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens 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, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 4, 4, 1, 1, 1, 1, 15, 15, 15] 50 rigid atoms, others: [33, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 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/316102/xbz-8058115.52/working/building/ZINC001635631282 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/31 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001635631282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635631282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001635631282 none C=C(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens 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, 7, 3, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 1, 4, 4, 1, 1, 1, 1, 15, 15, 15] 50 rigid atoms, others: [33, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001635631282 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282 Building ZINC001635631282 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635631282 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 30) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001635631282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635631282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001635631282 none C=C(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens 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, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 4, 4, 1, 1, 1, 1, 15, 15, 15] 50 rigid atoms, others: [33, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 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/316102/xbz-8058115.52/working/building/ZINC001635631282 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 31) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001635631282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635631282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001635631282 none C=C(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens 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, 7, 3, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 1, 4, 4, 1, 1, 1, 1, 15, 15, 15] 50 rigid atoms, others: [33, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001635631282 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001635631282 Building ZINC001638656626 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638656626 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/32 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(O)CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001638656626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638656626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638656626 none C=CCC1(O)CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 5, 14, 14, 14, 14, 14, 15, 5, 5, 5, 5, 2, 5, 5, 2, 2, 2, 2, 5, 5, 5, 5] 150 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/33 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001638656626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638656626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638656626 none C=CCC1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 14, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 6, 6, 17, 17, 17, 14, 14, 18, 6, 6, 6, 6, 2, 5, 5, 2, 2, 2, 2, 6, 6, 6, 6] 150 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001638656626 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626 Building ZINC001638656626 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638656626 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 32) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=CCC1(O)CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001638656626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638656626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638656626 none C=CCC1(O)CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 5, 14, 14, 14, 14, 14, 15, 5, 5, 5, 5, 2, 5, 5, 2, 2, 2, 2, 5, 5, 5, 5] 150 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 33) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=CCC1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001638656626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638656626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001638656626 none C=CCC1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 14, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 6, 6, 17, 17, 17, 14, 14, 18, 6, 6, 6, 6, 2, 5, 5, 2, 2, 2, 2, 6, 6, 6, 6] 150 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001638656626 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638656626 Building ZINC001638791284 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638791284 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/34 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](CC#N)C(F)(F)F) `ZINC001638791284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638791284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001638791284 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](CC#N)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.1', 'N.1', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 15, 15, 8, 8, 8, 8, 4, 4, 4, 4, 14, 14, 4, 3, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/35 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](CC#N)C(F)(F)F) `ZINC001638791284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638791284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001638791284 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](CC#N)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.1', 'N.1', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 15, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 14, 14, 9, 9, 9, 9, 4, 4, 4, 4, 15, 15, 4, 3, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001638791284 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284 Building ZINC001638791284 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638791284 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 34) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](CC#N)C(F)(F)F) `ZINC001638791284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638791284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001638791284 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](CC#N)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.1', 'N.1', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 15, 15, 8, 8, 8, 8, 4, 4, 4, 4, 14, 14, 4, 3, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 35) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](CC#N)C(F)(F)F) `ZINC001638791284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638791284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001638791284 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](CC#N)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.1', 'N.1', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 15, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 14, 14, 9, 9, 9, 9, 4, 4, 4, 4, 15, 15, 4, 3, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001638791284 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791284 Building ZINC001638791285 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638791285 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/36 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC#N)C(F)(F)F) `ZINC001638791285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638791285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001638791285 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC#N)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.1', 'N.1', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 15, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 14, 14, 9, 9, 9, 9, 4, 4, 4, 4, 15, 15, 4, 3, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/37 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](CC#N)C(F)(F)F) `ZINC001638791285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638791285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001638791285 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](CC#N)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.1', 'N.1', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 15, 15, 8, 8, 8, 8, 4, 4, 4, 4, 14, 14, 4, 3, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001638791285 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285 Building ZINC001638791285 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638791285 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 36) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC#N)C(F)(F)F) `ZINC001638791285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638791285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001638791285 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC#N)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.1', 'N.1', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 15, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 14, 14, 9, 9, 9, 9, 4, 4, 4, 4, 15, 15, 4, 3, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 37) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](CC#N)C(F)(F)F) `ZINC001638791285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638791285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001638791285 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](CC#N)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.1', 'N.1', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 15, 15, 8, 8, 8, 8, 4, 4, 4, 4, 14, 14, 4, 3, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001638791285 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001638791285 Building ZINC001643372407 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643372407 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/38 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001643372407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643372407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001643372407 none C#CCNS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 22, 12, 22, 22, 12, 12, 12, 4, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 50, 50, 50, 34, 12, 12, 12, 12, 2, 2, 4, 2, 2, 12, 12, 12, 12] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/39 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001643372407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643372407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001643372407 none C#CCNS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 23, 13, 23, 23, 13, 13, 13, 4, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 35, 13, 13, 13, 13, 1, 1, 2, 1, 1, 13, 13, 13, 13] 100 rigid atoms, others: [32, 33, 35, 36, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 37, 38, 39, 40]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001643372407 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407 Building ZINC001643372407 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643372407 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 38) grep: /scratch/xiaobo/316102/xbz-8058115.52/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#CCNS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001643372407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643372407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001643372407 none C#CCNS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 22, 12, 22, 22, 12, 12, 12, 4, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 50, 50, 50, 34, 12, 12, 12, 12, 2, 2, 4, 2, 2, 12, 12, 12, 12] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 39) grep: /scratch/xiaobo/316102/xbz-8058115.52/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#CCNS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001643372407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643372407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001643372407 none C#CCNS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 23, 13, 23, 23, 13, 13, 13, 4, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 35, 13, 13, 13, 13, 1, 1, 2, 1, 1, 13, 13, 13, 13] 100 rigid atoms, others: [32, 33, 35, 36, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 37, 38, 39, 40]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001643372407 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643372407 Building ZINC001643516527 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643516527 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/40 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC1(O)CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001643516527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643516527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001643516527 none C#CCC1(O)CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.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: [1, 1, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 5, 12, 12, 12, 15, 5, 5, 5, 5, 2, 7, 7, 2, 2, 2, 2, 5, 5, 5, 5] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/41 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001643516527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643516527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001643516527 none C#CCC1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.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: [1, 1, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 5, 12, 12, 12, 15, 5, 5, 5, 5, 2, 5, 5, 2, 2, 2, 2, 5, 5, 5, 5] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001643516527 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527 Building ZINC001643516527 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643516527 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 40) grep: /scratch/xiaobo/316102/xbz-8058115.52/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#CCC1(O)CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001643516527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643516527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001643516527 none C#CCC1(O)CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.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: [1, 1, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 5, 12, 12, 12, 15, 5, 5, 5, 5, 2, 7, 7, 2, 2, 2, 2, 5, 5, 5, 5] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 41) grep: /scratch/xiaobo/316102/xbz-8058115.52/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#CCC1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001643516527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643516527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001643516527 none C#CCC1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.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: [1, 1, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 5, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 5, 12, 12, 12, 15, 5, 5, 5, 5, 2, 5, 5, 2, 2, 2, 2, 5, 5, 5, 5] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001643516527 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001643516527 Building ZINC001652016761 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001652016761 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/42 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001652016761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001652016761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001652016761 none C=CCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 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] 0 hydrogens 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, 23, 12, 11, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 5, 14, 14, 14, 29, 29, 29, 23, 23, 12, 12, 12, 12, 2, 1, 4, 4, 1, 1, 1, 1, 14, 14, 14] 50 rigid atoms, others: [36, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/43 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001652016761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001652016761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001652016761 none C=CCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 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] 0 hydrogens 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, 26, 17, 13, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 15, 15, 15, 32, 32, 32, 26, 26, 17, 16, 16, 16, 2, 1, 3, 3, 1, 1, 1, 1, 15, 15, 15] 50 rigid atoms, others: [36, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001652016761 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761 Building ZINC001652016761 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001652016761 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 42) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=CCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001652016761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001652016761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001652016761 none C=CCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 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] 0 hydrogens 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, 23, 12, 11, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 5, 14, 14, 14, 29, 29, 29, 23, 23, 12, 12, 12, 12, 2, 1, 4, 4, 1, 1, 1, 1, 14, 14, 14] 50 rigid atoms, others: [36, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 43) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=CCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001652016761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001652016761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001652016761 none C=CCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 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] 0 hydrogens 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, 26, 17, 13, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 15, 15, 15, 32, 32, 32, 26, 26, 17, 16, 16, 16, 2, 1, 3, 3, 1, 1, 1, 1, 15, 15, 15] 50 rigid atoms, others: [36, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001652016761 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016761 Building ZINC001652016768 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001652016768 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/44 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001652016768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001652016768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001652016768 none C=CCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 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] 0 hydrogens 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, 26, 17, 13, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 15, 15, 15, 32, 32, 32, 26, 26, 16, 17, 16, 16, 2, 1, 3, 3, 1, 1, 1, 1, 15, 15, 15] 50 rigid atoms, others: [36, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/45 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001652016768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001652016768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001652016768 none C=CCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 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] 0 hydrogens 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, 23, 12, 11, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 5, 14, 14, 14, 29, 29, 29, 23, 23, 12, 12, 12, 12, 2, 1, 4, 4, 1, 1, 1, 1, 14, 14, 14] 50 rigid atoms, others: [36, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001652016768 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768 Building ZINC001652016768 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001652016768 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 44) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=CCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001652016768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001652016768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001652016768 none C=CCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 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] 0 hydrogens 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, 26, 17, 13, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 15, 15, 15, 32, 32, 32, 26, 26, 16, 17, 16, 16, 2, 1, 3, 3, 1, 1, 1, 1, 15, 15, 15] 50 rigid atoms, others: [36, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 45) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=CCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC) `ZINC001652016768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001652016768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001652016768 none C=CCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 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] 0 hydrogens 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, 23, 12, 11, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 5, 14, 14, 14, 29, 29, 29, 23, 23, 12, 12, 12, 12, 2, 1, 4, 4, 1, 1, 1, 1, 14, 14, 14] 50 rigid atoms, others: [36, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001652016768 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001652016768 Building ZINC001682385924 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001682385924 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/46 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001682385924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001682385924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001682385924 none C=C(C)C[C@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 31, 15, 31, 31, 49, 49, 49, 8, 15, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/47 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001682385924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001682385924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001682385924 none C=C(C)C[C@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 16, 30, 30, 50, 50, 50, 7, 16, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001682385924 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924 Building ZINC001682385924 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001682385924 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 46) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001682385924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001682385924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001682385924 none C=C(C)C[C@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 31, 15, 31, 31, 49, 49, 49, 8, 15, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 47) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001682385924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001682385924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001682385924 none C=C(C)C[C@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 16, 30, 30, 50, 50, 50, 7, 16, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001682385924 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385924 Building ZINC001682385925 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001682385925 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/48 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001682385925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001682385925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001682385925 none C=C(C)C[C@@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 34, 16, 34, 34, 46, 46, 46, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 46, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/49 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001682385925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001682385925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001682385925 none C=C(C)C[C@@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 16, 30, 30, 47, 47, 47, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001682385925 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925 Building ZINC001682385925 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001682385925 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 48) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(C)C[C@@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001682385925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001682385925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001682385925 none C=C(C)C[C@@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 34, 16, 34, 34, 46, 46, 46, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 46, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 49) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(C)C[C@@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001682385925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001682385925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001682385925 none C=C(C)C[C@@H](NC(C)=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 16, 30, 30, 47, 47, 47, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001682385925 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001682385925 Building ZINC001691743398 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001691743398 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/50 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNC(=O)CNC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OCC) `ZINC001691743398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001691743398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001691743398 none C#CCNC(=O)CNC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 8, 1, 11, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 40, 34, 40, 22, 16, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 9, 11, 50, 50, 50, 40, 34, 34, 22, 16, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/51 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNC(=O)CNC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OCC) `ZINC001691743398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001691743398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001691743398 none C#CCNC(=O)CNC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 8, 1, 11, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 46, 36, 46, 21, 15, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 50, 50, 50, 46, 36, 36, 21, 15, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001691743398 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398 Building ZINC001691743398 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001691743398 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 50) grep: /scratch/xiaobo/316102/xbz-8058115.52/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#CCNC(=O)CNC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OCC) `ZINC001691743398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001691743398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001691743398 none C#CCNC(=O)CNC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 8, 1, 11, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 40, 34, 40, 22, 16, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 9, 11, 50, 50, 50, 40, 34, 34, 22, 16, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 51) grep: /scratch/xiaobo/316102/xbz-8058115.52/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#CCNC(=O)CNC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OCC) `ZINC001691743398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001691743398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001691743398 none C#CCNC(=O)CNC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 8, 1, 11, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 46, 36, 46, 21, 15, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 50, 50, 50, 46, 36, 36, 21, 15, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001691743398 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001691743398 Building ZINC001719261405 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719261405 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/52 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1) `ZINC001719261405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719261405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001719261405 none C=CCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 22, 22, 22, 12, 10, 12, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 22, 22, 50, 50, 50, 50, 50, 41, 41, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 219 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/53 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1) `ZINC001719261405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719261405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001719261405 none C=CCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 44, 21, 21, 21, 12, 9, 12, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 21, 21, 50, 50, 50, 50, 50, 44, 44, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719261405 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405 Building ZINC001719261405 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719261405 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 52) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=CCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1) `ZINC001719261405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719261405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001719261405 none C=CCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 22, 22, 22, 12, 10, 12, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 22, 22, 50, 50, 50, 50, 50, 41, 41, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 219 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 53) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=CCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1) `ZINC001719261405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719261405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001719261405 none C=CCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 44, 21, 21, 21, 12, 9, 12, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 21, 21, 50, 50, 50, 50, 50, 44, 44, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719261405 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719261405 Building ZINC001739420322 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739420322 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/54 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001739420322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739420322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739420322 none C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 14, 40, 40, 48, 48, 48, 14, 14, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/55 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001739420322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739420322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739420322 none C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 42, 16, 42, 42, 49, 49, 49, 16, 16, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001739420322 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322 Building ZINC001739420322 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739420322 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 54) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001739420322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739420322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739420322 none C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 14, 40, 40, 48, 48, 48, 14, 14, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 55) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001739420322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739420322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739420322 none C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 42, 16, 42, 42, 49, 49, 49, 16, 16, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001739420322 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420322 Building ZINC001739420323 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739420323 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/56 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001739420323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739420323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739420323 none C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 38, 11, 38, 38, 43, 43, 43, 11, 11, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 43, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/57 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001739420323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739420323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739420323 none C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 44, 15, 44, 44, 49, 49, 49, 15, 15, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001739420323 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323 Building ZINC001739420323 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739420323 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 56) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001739420323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739420323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739420323 none C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 38, 11, 38, 38, 43, 43, 43, 11, 11, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 43, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 57) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001739420323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739420323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739420323 none C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 44, 15, 44, 44, 49, 49, 49, 15, 15, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001739420323 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739420323 Building ZINC001739624718 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739624718 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/58 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001739624718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739624718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739624718 none C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 42, 11, 42, 42, 50, 50, 50, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/59 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001739624718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739624718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739624718 none C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 42, 13, 42, 42, 50, 50, 50, 13, 13, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001739624718 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718 Building ZINC001739624718 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739624718 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 58) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001739624718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739624718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739624718 none C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 42, 11, 42, 42, 50, 50, 50, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 59) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001739624718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739624718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739624718 none C=C(C)C[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 42, 13, 42, 42, 50, 50, 50, 13, 13, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001739624718 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624718 Building ZINC001739624719 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739624719 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/60 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001739624719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739624719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739624719 none C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 38, 13, 38, 38, 45, 45, 45, 13, 13, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 45, 45, 45, 45, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/61 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001739624719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739624719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739624719 none C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 15, 40, 40, 48, 48, 48, 15, 15, 6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001739624719 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719 Building ZINC001739624719 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001739624719 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 60) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001739624719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001739624719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739624719 none C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 38, 13, 38, 38, 45, 45, 45, 13, 13, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 45, 45, 45, 45, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 61) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001739624719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001739624719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001739624719 none C=C(C)C[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 15, 40, 40, 48, 48, 48, 15, 15, 6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001739624719 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001739624719 Building ZINC000146084632 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000146084632 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/62 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(c2cnccn2)c2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCNCC3)c21) `ZINC000146084632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000146084632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000146084632 none COc1cnc(c2cnccn2)c2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCNCC3)c21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 1, 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, 3, 7, 7, 7, 3, 7, 7, 3, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 7, 8, 8, 8, 7, 28, 28, 28, 7, 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]) total number of confs: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/63 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(c2cnccn2)c2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCNCC3)c21) `ZINC000146084632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000146084632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000146084632 none COc1cnc(c2cnccn2)c2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCNCC3)c21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 1, 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, 3, 7, 7, 7, 3, 7, 7, 3, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 36, 36, 36, 36, 36, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 36, 36, 36, 6, 8, 8, 8, 8, 8, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000146084632 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632 Building ZINC000146084632 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000146084632 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 62) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cnc(c2cnccn2)c2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCNCC3)c21) `ZINC000146084632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000146084632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000146084632 none COc1cnc(c2cnccn2)c2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCNCC3)c21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 1, 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, 3, 7, 7, 7, 3, 7, 7, 3, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 7, 8, 8, 8, 7, 28, 28, 28, 7, 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]) total number of confs: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 63) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cnc(c2cnccn2)c2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCNCC3)c21) `ZINC000146084632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000146084632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000146084632 none COc1cnc(c2cnccn2)c2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCNCC3)c21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 1, 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, 3, 7, 7, 7, 3, 7, 7, 3, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 36, 36, 36, 36, 36, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 36, 36, 36, 6, 8, 8, 8, 8, 8, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000146084632 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000146084632 Building ZINC000500218859 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000500218859 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/64 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCS(=O)(=O)CC1) `ZINC000500218859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000500218859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000500218859 none COC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 26, 50, 12, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 26, 26, 26, 26, 50, 50, 50, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26] 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/65 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCS(=O)(=O)CC1) `ZINC000500218859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000500218859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000500218859 none COC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 50, 12, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 5, 3, 3, 3, 3, 27, 27, 27, 27, 27, 27, 27, 27] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000500218859 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859 Building ZINC000500218859 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000500218859 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 64) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCS(=O)(=O)CC1) `ZINC000500218859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000500218859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000500218859 none COC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 26, 50, 12, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 26, 26, 26, 26, 50, 50, 50, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26] 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 65) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCS(=O)(=O)CC1) `ZINC000500218859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000500218859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000500218859 none COC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 50, 12, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 5, 3, 3, 3, 3, 27, 27, 27, 27, 27, 27, 27, 27] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000500218859 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500218859 Building ZINC000500391954 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000500391954 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/66 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](C(N)=O)N(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000500391954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000500391954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000500391954 none COC[C@@H](C(N)=O)N(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.am', 'C.3', '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, 12, 5, 5, 7, 1, 8, 11, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 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, 4, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 8, 3, 8, 8, 17, 17, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 31, 31, 31, 25, 25, 17, 17, 3, 3, 3, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/67 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](C(N)=O)N(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000500391954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000500391954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000500391954 none COC[C@@H](C(N)=O)N(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.am', 'C.3', '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, 12, 5, 5, 7, 1, 8, 11, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 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, 4, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 9, 4, 9, 9, 18, 18, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 33, 33, 33, 25, 25, 18, 18, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000500391954 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954 Building ZINC000500391954 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000500391954 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 66) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC[C@@H](C(N)=O)N(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000500391954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000500391954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000500391954 none COC[C@@H](C(N)=O)N(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.am', 'C.3', '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, 12, 5, 5, 7, 1, 8, 11, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 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, 4, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 8, 3, 8, 8, 17, 17, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 31, 31, 31, 25, 25, 17, 17, 3, 3, 3, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 67) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC[C@@H](C(N)=O)N(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000500391954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000500391954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000500391954 none COC[C@@H](C(N)=O)N(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'N.am', 'C.3', '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, 12, 5, 5, 7, 1, 8, 11, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 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, 4, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 9, 4, 9, 9, 18, 18, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 33, 33, 33, 25, 25, 18, 18, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000500391954 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500391954 Building ZINC000500491868 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000500491868 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/68 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)nn1) `ZINC000500491868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000500491868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000500491868 none COC(=O)c1cn(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 26, 17, 17, 4, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 17, 17, 26, 26, 26, 17, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/69 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn(C2CN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)nn1) `ZINC000500491868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000500491868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000500491868 none COC(=O)c1cn(C2CN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 28, 14, 14, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 28, 28, 28, 14, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000500491868 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868 Building ZINC000500491868 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000500491868 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 68) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)c1cn(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)nn1) `ZINC000500491868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000500491868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000500491868 none COC(=O)c1cn(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 26, 17, 17, 4, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 17, 17, 26, 26, 26, 17, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 69) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)c1cn(C2CN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)nn1) `ZINC000500491868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000500491868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000500491868 none COC(=O)c1cn(C2CN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 28, 14, 14, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 28, 28, 28, 14, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000500491868 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500491868 Building ZINC000500575997 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000500575997 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/70 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn(C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)nn1) `ZINC000500575997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000500575997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000500575997 none COC(=O)c1cn(C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 18, 18, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 2, 18, 18, 31, 31, 31, 18, 2, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/71 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn(C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)nn1) `ZINC000500575997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000500575997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000500575997 none COC(=O)c1cn(C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 2, 20, 20, 33, 33, 33, 20, 2, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000500575997 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997 Building ZINC000500575997 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000500575997 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 70) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)c1cn(C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)nn1) `ZINC000500575997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000500575997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000500575997 none COC(=O)c1cn(C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 18, 18, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 2, 18, 18, 31, 31, 31, 18, 2, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 71) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)c1cn(C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)nn1) `ZINC000500575997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000500575997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000500575997 none COC(=O)c1cn(C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 2, 20, 20, 33, 33, 33, 20, 2, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000500575997 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000500575997 Building ZINC000501999100 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000501999100 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/72 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCS(=O)(=O)N1CCSCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000501999100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000501999100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000501999100 none O=C(NCCS(=O)(=O)N1CCSCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 8, 5, 5, 14, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 14, 27, 27, 36, 50, 50, 50, 50, 45, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/73 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCS(=O)(=O)N1CCSCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000501999100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000501999100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000501999100 none O=C(NCCS(=O)(=O)N1CCSCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 8, 5, 5, 14, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 26, 26, 37, 50, 50, 50, 50, 45, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000501999100 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100 Building ZINC000501999100 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000501999100 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 72) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCS(=O)(=O)N1CCSCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000501999100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000501999100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000501999100 none O=C(NCCS(=O)(=O)N1CCSCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 8, 5, 5, 14, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 14, 27, 27, 36, 50, 50, 50, 50, 45, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 73) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCS(=O)(=O)N1CCSCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000501999100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000501999100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000501999100 none O=C(NCCS(=O)(=O)N1CCSCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 8, 5, 5, 14, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 26, 26, 37, 50, 50, 50, 50, 45, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000501999100 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000501999100 Building ZINC001280752931 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001280752931 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/74 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001280752931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001280752931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001280752931 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 24, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 48, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/75 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001280752931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001280752931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001280752931 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 24, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 49, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 8, 39, 34, 40, 35, 7, 36, 6, 5, 37, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001280752931 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931 Building ZINC001280752931 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001280752931 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 74) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001280752931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001280752931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001280752931 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 24, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 48, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 75) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001280752931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001280752931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001280752931 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 24, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 49, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 8, 39, 34, 40, 35, 7, 36, 6, 5, 37, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001280752931 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280752931 Building ZINC001719583959 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719583959 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/76 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC001719583959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719583959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001719583959 none COC[C@@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 12, 34, 34, 40, 8, 12, 8, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50, 50, 50, 48, 48, 40, 40, 40, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/77 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC001719583959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719583959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001719583959 none COC[C@@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 35, 15, 35, 35, 44, 10, 15, 10, 10, 10, 10, 10, 9, 2, 9, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 50, 50, 50, 49, 49, 44, 44, 44, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719583959 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959 Building ZINC001719583959 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719583959 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 76) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC[C@@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC001719583959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719583959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001719583959 none COC[C@@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 12, 34, 34, 40, 8, 12, 8, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50, 50, 50, 48, 48, 40, 40, 40, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 77) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC[C@@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC001719583959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719583959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001719583959 none COC[C@@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 35, 15, 35, 35, 44, 10, 15, 10, 10, 10, 10, 10, 9, 2, 9, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 50, 50, 50, 49, 49, 44, 44, 44, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719583959 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583959 Building ZINC001719583960 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719583960 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/78 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC001719583960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719583960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001719583960 none COC[C@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 15, 34, 34, 40, 7, 15, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 49, 49, 40, 40, 40, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/79 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC001719583960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719583960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001719583960 none COC[C@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 19, 40, 40, 42, 12, 19, 12, 12, 12, 12, 12, 11, 2, 11, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 42, 42, 42, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719583960 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960 Building ZINC001719583960 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719583960 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 78) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC[C@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC001719583960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719583960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001719583960 none COC[C@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 15, 34, 34, 40, 7, 15, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 49, 49, 40, 40, 40, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 79) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC[C@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC001719583960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719583960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001719583960 none COC[C@H](OC)C(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 19, 40, 40, 42, 12, 19, 12, 12, 12, 12, 12, 11, 2, 11, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 42, 42, 42, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719583960 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719583960 Building ZINC001280768544 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001280768544 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/80 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001280768544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001280768544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001280768544 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 28, 28, 28, 28, 28, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 46, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 8, 9, 39, 34, 40, 35, 7, 36, 6, 5, 37, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/81 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001280768544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001280768544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001280768544 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 12, 28, 28, 28, 28, 28, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 48, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 8, 9, 39, 34, 40, 35, 7, 36, 6, 5, 37, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001280768544 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544 Building ZINC001280768544 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001280768544 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 80) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001280768544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001280768544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001280768544 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 28, 28, 28, 28, 28, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 46, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 8, 9, 39, 34, 40, 35, 7, 36, 6, 5, 37, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 81) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001280768544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001280768544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001280768544 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 12, 28, 28, 28, 28, 28, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 48, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 8, 9, 39, 34, 40, 35, 7, 36, 6, 5, 37, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001280768544 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280768544 Building ZINC001701094850 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701094850 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/82 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001701094850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701094850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001701094850 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 24, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 49, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 8, 39, 34, 40, 35, 7, 36, 6, 5, 37, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/83 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001701094850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701094850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001701094850 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 24, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 48, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701094850 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850 Building ZINC001701094850 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701094850 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 82) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001701094850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701094850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001701094850 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 24, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 49, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 8, 39, 34, 40, 35, 7, 36, 6, 5, 37, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 83) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001701094850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701094850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001701094850 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 24, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 48, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701094850 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701094850 Building ZINC000482671535 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482671535 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/84 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(=O)OC) `ZINC000482671535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482671535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000482671535 none COC(=O)CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 35, 9, 6, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 6, 15, 15, 15, 35, 35, 35, 13, 15, 11, 11, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 15, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/85 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(=O)OC) `ZINC000482671535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482671535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000482671535 none COC(=O)CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 38, 10, 6, 2, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 6, 13, 13, 13, 38, 38, 38, 17, 15, 12, 12, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000482671535 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535 Building ZINC000482671535 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482671535 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 84) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(=O)OC) `ZINC000482671535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482671535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000482671535 none COC(=O)CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 35, 9, 6, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 6, 15, 15, 15, 35, 35, 35, 13, 15, 11, 11, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 15, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 85) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(=O)OC) `ZINC000482671535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482671535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000482671535 none COC(=O)CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 38, 10, 6, 2, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 6, 13, 13, 13, 38, 38, 38, 17, 15, 12, 12, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000482671535 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000482671535 Building ZINC001520725538 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520725538 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/86 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001520725538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520725538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520725538 none CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 42, 45, 45, 18, 18, 18, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 42, 42, 18, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/87 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001520725538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520725538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520725538 none CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 43, 47, 47, 15, 15, 15, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 43, 43, 15, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520725538 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538 Building ZINC001520725538 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520725538 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 86) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001520725538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520725538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520725538 none CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 42, 45, 45, 18, 18, 18, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 42, 42, 18, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 87) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001520725538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520725538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520725538 none CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 43, 47, 47, 15, 15, 15, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 43, 43, 15, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520725538 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520725538 Building ZINC000504487890 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000504487890 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/88 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000504487890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000504487890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000504487890 none NS(=O)(=O)CCCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 49, 28, 18, 20, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 37, 37, 25, 28, 24, 24, 20, 20, 5, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/89 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000504487890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000504487890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000504487890 none NS(=O)(=O)CCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 49, 28, 18, 20, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 2, 3, 3, 49, 49, 37, 37, 28, 25, 24, 24, 20, 20, 5, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000504487890 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890 Building ZINC000504487890 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000504487890 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 88) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: NS(=O)(=O)CCCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000504487890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000504487890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000504487890 none NS(=O)(=O)CCCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 49, 28, 18, 20, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 37, 37, 25, 28, 24, 24, 20, 20, 5, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 89) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: NS(=O)(=O)CCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000504487890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000504487890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000504487890 none NS(=O)(=O)CCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 49, 28, 18, 20, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 2, 3, 3, 49, 49, 37, 37, 28, 25, 24, 24, 20, 20, 5, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000504487890 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000504487890 Building ZINC001539755693 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001539755693 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/90 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Cl)s1) `ZINC001539755693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001539755693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001539755693 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 11, 23, 23, 23, 23, 23, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 22, 23, 24, 25, 28] set([32, 33, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/91 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Cl)s1) `ZINC001539755693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001539755693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001539755693 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 11, 23, 23, 23, 23, 23, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 22, 23, 24, 25, 28] set([32, 33, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001539755693 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693 Building ZINC001539755693 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001539755693 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 90) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Cl)s1) `ZINC001539755693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001539755693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001539755693 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 11, 23, 23, 23, 23, 23, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 22, 23, 24, 25, 28] set([32, 33, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 91) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Cl)s1) `ZINC001539755693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001539755693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001539755693 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 11, 23, 23, 23, 23, 23, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 22, 23, 24, 25, 28] set([32, 33, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001539755693 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001539755693 Building ZINC000857768544 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000857768544 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/92 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNCCCC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)CC1) `ZINC000857768544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000857768544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000857768544 none CNCCCC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 27, 15, 11, 15, 11, 11, 11, 6, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 50, 50, 50, 50, 50, 50, 31, 31, 27, 27, 11, 11, 11, 11, 11, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 227 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/93 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNCCCC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])C2CCSCC2)CC1) `ZINC000857768544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000857768544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000857768544 none CNCCCC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])C2CCSCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 48, 30, 27, 15, 14, 15, 14, 14, 14, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 49, 49, 49, 49, 48, 48, 30, 30, 27, 27, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000857768544 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544 Building ZINC000857768544 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000857768544 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 92) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNCCCC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)CC1) `ZINC000857768544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000857768544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000857768544 none CNCCCC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 27, 15, 11, 15, 11, 11, 11, 6, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 50, 50, 50, 50, 50, 50, 31, 31, 27, 27, 11, 11, 11, 11, 11, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 227 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 93) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNCCCC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])C2CCSCC2)CC1) `ZINC000857768544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000857768544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000857768544 none CNCCCC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])C2CCSCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 48, 30, 27, 15, 14, 15, 14, 14, 14, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 49, 49, 49, 49, 48, 48, 30, 30, 27, 27, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000857768544 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000857768544 Building ZINC000408118846 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408118846 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/94 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCN1S(C)(=O)=O) `ZINC000408118846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408118846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000408118846 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCN1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 10, 1, 8, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 17, 17, 17, 17, 28, 28, 28, 17, 17, 17, 17, 17, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 17, 17, 17, 17, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/95 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCN1S(C)(=O)=O) `ZINC000408118846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408118846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000408118846 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCN1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 9, 2, 8, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 16, 16, 16, 16, 27, 27, 27, 16, 16, 16, 16, 16, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 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, 43, 44, 45, 46, 47]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000408118846 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846 Building ZINC000408118846 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000408118846 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 94) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCN1S(C)(=O)=O) `ZINC000408118846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000408118846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000408118846 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCN1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 10, 1, 8, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 17, 17, 17, 17, 28, 28, 28, 17, 17, 17, 17, 17, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 17, 17, 17, 17, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 95) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCN1S(C)(=O)=O) `ZINC000408118846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000408118846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000408118846 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCN1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 9, 2, 8, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 16, 16, 16, 16, 27, 27, 27, 16, 16, 16, 16, 16, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 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, 43, 44, 45, 46, 47]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000408118846 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000408118846 Building ZINC000240773460 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000240773460 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/96 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])CCOc1ccccc1)N1CCN(C2CC2)CC1) `ZINC000240773460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000240773460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000240773460 none O=C(CNC(=O)[C@]([O-])([SiH3])CCOc1ccccc1)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 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: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 12, 14, 14, 14, 14, 14, 15, 24, 24, 24, 24, 25, 25, 24, 24, 4, 4, 2, 4, 4, 4, 4, 14, 14, 14, 14, 14, 24, 24, 24, 24, 25, 25, 25, 25, 25, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 88 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/97 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])CCOc1ccccc1)N1CCN(C2CC2)CC1) `ZINC000240773460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000240773460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000240773460 none O=C(CNC(=O)[C@@]([O-])([SiH3])CCOc1ccccc1)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 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: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 11, 13, 13, 11, 13, 13, 15, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 2, 4, 4, 4, 4, 13, 13, 11, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 84 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000240773460 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460 Building ZINC000240773460 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000240773460 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 96) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@]([O-])([SiH3])CCOc1ccccc1)N1CCN(C2CC2)CC1) `ZINC000240773460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000240773460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000240773460 none O=C(CNC(=O)[C@]([O-])([SiH3])CCOc1ccccc1)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 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: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 12, 14, 14, 14, 14, 14, 15, 24, 24, 24, 24, 25, 25, 24, 24, 4, 4, 2, 4, 4, 4, 4, 14, 14, 14, 14, 14, 24, 24, 24, 24, 25, 25, 25, 25, 25, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 88 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 97) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@@]([O-])([SiH3])CCOc1ccccc1)N1CCN(C2CC2)CC1) `ZINC000240773460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000240773460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000240773460 none O=C(CNC(=O)[C@@]([O-])([SiH3])CCOc1ccccc1)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 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: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 11, 13, 13, 11, 13, 13, 15, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 2, 4, 4, 4, 4, 13, 13, 11, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 84 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000240773460 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000240773460 Building ZINC000242455646 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242455646 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/98 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1cccnc1)N1CCN(c2cccc(F)c2)CC1) `ZINC000242455646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242455646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242455646 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1cccnc1)N1CCN(c2cccc(F)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 16, 19, 19, 19, 19, 30, 30, 30, 30, 30, 30, 19, 19, 10, 10, 4, 4, 4, 4, 4, 19, 19, 19, 19, 30, 30, 30, 30, 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]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/99 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1cccnc1)N1CCN(c2cccc(F)c2)CC1) `ZINC000242455646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242455646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242455646 none O=C(CNC(=O)[C@]([O-])([SiH3])c1cccnc1)N1CCN(c2cccc(F)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 29, 29, 29, 29, 29, 29, 16, 16, 10, 10, 4, 4, 4, 4, 4, 16, 16, 16, 16, 29, 29, 29, 29, 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]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242455646 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646 Building ZINC000242455646 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242455646 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 98) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1cccnc1)N1CCN(c2cccc(F)c2)CC1) `ZINC000242455646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242455646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242455646 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1cccnc1)N1CCN(c2cccc(F)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 16, 19, 19, 19, 19, 30, 30, 30, 30, 30, 30, 19, 19, 10, 10, 4, 4, 4, 4, 4, 19, 19, 19, 19, 30, 30, 30, 30, 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]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 99) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1cccnc1)N1CCN(c2cccc(F)c2)CC1) `ZINC000242455646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242455646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242455646 none O=C(CNC(=O)[C@]([O-])([SiH3])c1cccnc1)N1CCN(c2cccc(F)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 29, 29, 29, 29, 29, 29, 16, 16, 10, 10, 4, 4, 4, 4, 4, 16, 16, 16, 16, 29, 29, 29, 29, 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]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242455646 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242455646 Building ZINC000242628490 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242628490 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/100 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C[C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1) `ZINC000242628490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242628490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000242628490 none COc1ccc(C[C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 1, 1, 1, 2, 2, 2, 11, 24, 32, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 11, 11, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/101 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C[C@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1) `ZINC000242628490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242628490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000242628490 none COc1ccc(C[C@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 1, 1, 1, 2, 2, 2, 10, 22, 35, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 10, 10, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242628490 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490 Building ZINC000242628490 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242628490 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 100) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccc(C[C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1) `ZINC000242628490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242628490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000242628490 none COc1ccc(C[C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 1, 1, 1, 2, 2, 2, 11, 24, 32, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 11, 11, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 101) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccc(C[C@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1) `ZINC000242628490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242628490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000242628490 none COc1ccc(C[C@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 1, 1, 1, 2, 2, 2, 10, 22, 35, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 10, 10, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242628490 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242628490 Building ZINC000242744594 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242744594 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/102 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])C2CCOCC2)CC1) `ZINC000242744594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242744594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000242744594 none Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])C2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 45, 45, 43, 43, 43, 43, 24, 14, 33, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 43, 43, 45, 45, 45, 45, 44, 45, 45, 43, 43, 43, 43, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 43, 43, 43, 43] 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, 53]) total number of confs: 134 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/103 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])C2CCOCC2)CC1) `ZINC000242744594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242744594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000242744594 none Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])C2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 45, 45, 45, 45, 26, 15, 36, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 45, 45, 46, 46, 46, 46, 46, 46, 46, 45, 45, 45, 45, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 45, 45, 45, 45] 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, 53]) total number of confs: 133 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242744594 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594 Building ZINC000242744594 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242744594 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 102) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])C2CCOCC2)CC1) `ZINC000242744594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242744594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000242744594 none Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])C2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 45, 45, 43, 43, 43, 43, 24, 14, 33, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 43, 43, 45, 45, 45, 45, 44, 45, 45, 43, 43, 43, 43, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 43, 43, 43, 43] 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, 53]) total number of confs: 134 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 103) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])C2CCOCC2)CC1) `ZINC000242744594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242744594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000242744594 none Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])C2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 45, 45, 45, 45, 26, 15, 36, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 45, 45, 46, 46, 46, 46, 46, 46, 46, 45, 45, 45, 45, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 45, 45, 45, 45] 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, 53]) total number of confs: 133 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242744594 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242744594 Building ZINC000242762556 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242762556 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/104 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2)CC1) `ZINC000242762556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242762556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242762556 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 33, 33, 33, 33, 33, 32, 32, 10, 10, 3, 5, 5, 5, 5, 32, 32, 32, 32, 33, 33, 33, 33, 33, 32, 32, 32, 32] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 87 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/105 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2)CC1) `ZINC000242762556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242762556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242762556 none O=C(CNC(=O)[C@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 18, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 33, 33, 33, 33, 33, 32, 32, 11, 11, 3, 5, 5, 5, 5, 32, 32, 32, 32, 33, 33, 33, 33, 33, 32, 32, 32, 32] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 89 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242762556 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556 Building ZINC000242762556 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242762556 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 104) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(CNC(=O)[C@@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2)CC1) `ZINC000242762556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242762556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242762556 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 33, 33, 33, 33, 33, 32, 32, 10, 10, 3, 5, 5, 5, 5, 32, 32, 32, 32, 33, 33, 33, 33, 33, 32, 32, 32, 32] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 87 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 105) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(CNC(=O)[C@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2)CC1) `ZINC000242762556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242762556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242762556 none O=C(CNC(=O)[C@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 18, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 33, 33, 33, 33, 33, 32, 32, 11, 11, 3, 5, 5, 5, 5, 32, 32, 32, 32, 33, 33, 33, 33, 33, 32, 32, 32, 32] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 89 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242762556 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242762556 Building ZINC001520752454 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001520752454 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/106 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 33, 33, 33, 31, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 13, 33, 33, 36, 36, 36, 36, 36, 33, 33, 33, 33, 13, 13, 13, 4, 8, 8, 4, 8, 8, 4, 13, 13, 33, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/107 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 32, 32, 32, 30, 12, 12, 12, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 9, 9, 5, 12, 32, 32, 35, 35, 35, 35, 35, 32, 32, 32, 32, 12, 12, 12, 5, 9, 9, 5, 9, 9, 5, 12, 12, 32, 32, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/108 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/108' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 29, 29, 29, 26, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 13, 29, 29, 34, 34, 34, 34, 34, 29, 29, 29, 29, 13, 13, 13, 4, 8, 8, 4, 8, 8, 4, 13, 13, 29, 29, 29, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/109 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/109' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 30, 30, 30, 28, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 13, 30, 30, 35, 35, 35, 35, 35, 30, 30, 30, 30, 13, 13, 13, 4, 7, 7, 4, 7, 7, 4, 13, 13, 30, 30, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520752454 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 Building ZINC001520752454 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001520752454 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 106) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[N@]1CC[N@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 33, 33, 33, 31, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 13, 33, 33, 36, 36, 36, 36, 36, 33, 33, 33, 33, 13, 13, 13, 4, 8, 8, 4, 8, 8, 4, 13, 13, 33, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 107) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[N@]1CC[N@@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 32, 32, 32, 30, 12, 12, 12, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 9, 9, 5, 12, 32, 32, 35, 35, 35, 35, 35, 32, 32, 32, 32, 12, 12, 12, 5, 9, 9, 5, 9, 9, 5, 12, 12, 32, 32, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 108) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 29, 29, 29, 26, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 13, 29, 29, 34, 34, 34, 34, 34, 29, 29, 29, 29, 13, 13, 13, 4, 8, 8, 4, 8, 8, 4, 13, 13, 29, 29, 29, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 109) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 30, 30, 30, 28, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 13, 30, 30, 35, 35, 35, 35, 35, 30, 30, 30, 30, 13, 13, 13, 4, 7, 7, 4, 7, 7, 4, 13, 13, 30, 30, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520752454 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 Building ZINC001520752454 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001520752454 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 106) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[N@]1CC[N@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 33, 33, 33, 31, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 13, 33, 33, 36, 36, 36, 36, 36, 33, 33, 33, 33, 13, 13, 13, 4, 8, 8, 4, 8, 8, 4, 13, 13, 33, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 107) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[N@]1CC[N@@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 32, 32, 32, 30, 12, 12, 12, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 9, 9, 5, 12, 32, 32, 35, 35, 35, 35, 35, 32, 32, 32, 32, 12, 12, 12, 5, 9, 9, 5, 9, 9, 5, 12, 12, 32, 32, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 108) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 29, 29, 29, 26, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 13, 29, 29, 34, 34, 34, 34, 34, 29, 29, 29, 29, 13, 13, 13, 4, 8, 8, 4, 8, 8, 4, 13, 13, 29, 29, 29, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 109) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 30, 30, 30, 28, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 13, 30, 30, 35, 35, 35, 35, 35, 30, 30, 30, 30, 13, 13, 13, 4, 7, 7, 4, 7, 7, 4, 13, 13, 30, 30, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520752454 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 Building ZINC001520752454 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001520752454 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 106) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[N@]1CC[N@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 33, 33, 33, 31, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 13, 33, 33, 36, 36, 36, 36, 36, 33, 33, 33, 33, 13, 13, 13, 4, 8, 8, 4, 8, 8, 4, 13, 13, 33, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 107) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[N@]1CC[N@@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@@](C2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 32, 32, 32, 30, 12, 12, 12, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 9, 9, 5, 12, 32, 32, 35, 35, 35, 35, 35, 32, 32, 32, 32, 12, 12, 12, 5, 9, 9, 5, 9, 9, 5, 12, 12, 32, 32, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 108) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 29, 29, 29, 26, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 13, 29, 29, 34, 34, 34, 34, 34, 29, 29, 29, 29, 13, 13, 13, 4, 8, 8, 4, 8, 8, 4, 13, 13, 29, 29, 29, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 109) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1) `ZINC001520752454.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001520752454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001520752454 none CC[N@]1CC[N@@](C2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 30, 30, 30, 28, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 13, 30, 30, 35, 35, 35, 35, 35, 30, 30, 30, 30, 13, 13, 13, 4, 7, 7, 4, 7, 7, 4, 13, 13, 30, 30, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520752454 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520752454 Building ZINC000242772385 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242772385 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/110 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])[C@@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1) `ZINC000242772385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242772385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242772385 none O=C(CNC(=O)[C@@]([O-])([SiH3])[C@@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 32, 32, 32, 32, 32, 35, 35, 32, 35, 35, 35, 32, 32, 11, 11, 3, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32, 35, 35, 35, 35, 32, 32, 32, 32] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/111 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])[C@@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1) `ZINC000242772385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242772385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242772385 none O=C(CNC(=O)[C@]([O-])([SiH3])[C@@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 21, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 48, 48, 46, 46, 48, 48, 46, 46, 13, 13, 4, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 48, 48, 48, 48, 46, 46, 46, 46] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242772385 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385 Building ZINC000242772385 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242772385 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 110) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@@]([O-])([SiH3])[C@@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1) `ZINC000242772385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242772385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242772385 none O=C(CNC(=O)[C@@]([O-])([SiH3])[C@@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 32, 32, 32, 32, 32, 35, 35, 32, 35, 35, 35, 32, 32, 11, 11, 3, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32, 35, 35, 35, 35, 32, 32, 32, 32] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 111) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@]([O-])([SiH3])[C@@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1) `ZINC000242772385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242772385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242772385 none O=C(CNC(=O)[C@]([O-])([SiH3])[C@@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 21, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 48, 48, 46, 46, 48, 48, 46, 46, 13, 13, 4, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 48, 48, 48, 48, 46, 46, 46, 46] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242772385 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772385 Building ZINC000242772386 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242772386 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/112 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])[C@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1) `ZINC000242772386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242772386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242772386 none O=C(CNC(=O)[C@@]([O-])([SiH3])[C@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 48, 48, 46, 48, 48, 48, 46, 46, 14, 14, 4, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 48, 48, 48, 48, 46, 46, 46, 46] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/113 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])[C@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1) `ZINC000242772386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242772386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242772386 none O=C(CNC(=O)[C@]([O-])([SiH3])[C@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 18, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 36, 36, 36, 36, 36, 36, 33, 33, 10, 10, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 36, 36, 36, 36, 33, 33, 33, 33] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242772386 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386 Building ZINC000242772386 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242772386 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 112) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@@]([O-])([SiH3])[C@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1) `ZINC000242772386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242772386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242772386 none O=C(CNC(=O)[C@@]([O-])([SiH3])[C@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 48, 48, 46, 48, 48, 48, 46, 46, 14, 14, 4, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 48, 48, 48, 48, 46, 46, 46, 46] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 113) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@]([O-])([SiH3])[C@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1) `ZINC000242772386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242772386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242772386 none O=C(CNC(=O)[C@]([O-])([SiH3])[C@H]1CCCO1)N1CCN(c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 18, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 36, 36, 36, 36, 36, 36, 33, 33, 10, 10, 3, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 36, 36, 36, 36, 33, 33, 33, 33] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242772386 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242772386 Building ZINC000506666643 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506666643 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/114 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506666643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506666643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666643 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 12, 12, 12, 12, 12, 12, 12, 26, 49, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 26, 26, 49, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/115 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506666643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506666643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666643 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 29, 48, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 6, 17, 17, 17, 17, 17, 17, 29, 29, 48, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506666643 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643 Building ZINC000506666643 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506666643 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 114) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506666643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506666643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666643 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 12, 12, 12, 12, 12, 12, 12, 26, 49, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 26, 26, 49, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 115) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506666643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506666643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666643 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 29, 48, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 6, 17, 17, 17, 17, 17, 17, 29, 29, 48, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506666643 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666643 Building ZINC000506666644 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506666644 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/116 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506666644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506666644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666644 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 30, 48, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 6, 17, 17, 17, 17, 17, 17, 30, 30, 48, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/117 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506666644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506666644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666644 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 11, 11, 11, 11, 11, 11, 11, 26, 48, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 11, 11, 26, 26, 48, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506666644 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644 Building ZINC000506666644 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506666644 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 116) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506666644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506666644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666644 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 30, 48, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 6, 17, 17, 17, 17, 17, 17, 30, 30, 48, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 117) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506666644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506666644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666644 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 11, 11, 11, 11, 11, 11, 11, 26, 48, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 11, 11, 26, 26, 48, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506666644 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666644 Building ZINC000506666645 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506666645 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/118 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506666645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506666645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666645 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 7, 19, 19, 19, 19, 19, 19, 19, 37, 48, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 19, 19, 19, 19, 19, 19, 37, 37, 48, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/119 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506666645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506666645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666645 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 18, 18, 18, 18, 18, 18, 18, 36, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 4, 18, 18, 18, 18, 18, 18, 36, 36, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506666645 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645 Building ZINC000506666645 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506666645 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 118) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506666645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506666645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666645 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 7, 19, 19, 19, 19, 19, 19, 19, 37, 48, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 19, 19, 19, 19, 19, 19, 37, 37, 48, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 119) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506666645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506666645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666645 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 18, 18, 18, 18, 18, 18, 18, 36, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 4, 18, 18, 18, 18, 18, 18, 36, 36, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506666645 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666645 Building ZINC000506666646 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506666646 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/120 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506666646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506666646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666646 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 17, 17, 17, 17, 17, 17, 17, 34, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 4, 17, 17, 17, 17, 17, 17, 34, 34, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/121 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506666646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506666646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666646 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 18, 18, 18, 18, 18, 18, 18, 37, 48, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 4, 18, 18, 18, 18, 18, 18, 37, 37, 48, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506666646 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646 Building ZINC000506666646 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506666646 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 120) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506666646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506666646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666646 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 17, 17, 17, 17, 17, 17, 17, 34, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 4, 17, 17, 17, 17, 17, 17, 34, 34, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 121) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506666646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506666646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506666646 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 18, 18, 18, 18, 18, 18, 18, 37, 48, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 4, 18, 18, 18, 18, 18, 18, 37, 37, 48, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506666646 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506666646 Building ZINC000506675283 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506675283 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/122 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506675283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506675283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675283 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 14, 14, 14, 14, 14, 14, 14, 33, 43, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 33, 33, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/123 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506675283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506675283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675283 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 19, 19, 19, 19, 19, 19, 19, 36, 46, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 19, 19, 19, 19, 19, 19, 36, 36, 46, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506675283 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283 Building ZINC000506675283 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506675283 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 122) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506675283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506675283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675283 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 14, 14, 14, 14, 14, 14, 14, 33, 43, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 33, 33, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 123) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506675283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506675283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675283 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 19, 19, 19, 19, 19, 19, 19, 36, 46, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 19, 19, 19, 19, 19, 19, 36, 36, 46, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506675283 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675283 Building ZINC000506675284 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506675284 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/124 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506675284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506675284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675284 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 15, 15, 15, 15, 15, 15, 15, 35, 46, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 15, 15, 15, 15, 15, 15, 35, 35, 46, 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]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/125 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506675284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506675284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675284 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 15, 15, 15, 15, 15, 15, 15, 32, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 32, 32, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506675284 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284 Building ZINC000506675284 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506675284 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 124) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506675284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506675284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675284 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 15, 15, 15, 15, 15, 15, 15, 35, 46, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 15, 15, 15, 15, 15, 15, 35, 35, 46, 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]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 125) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506675284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506675284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675284 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 15, 15, 15, 15, 15, 15, 15, 32, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 32, 32, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506675284 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675284 Building ZINC000506675285 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506675285 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/126 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506675285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506675285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675285 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 12, 12, 12, 12, 12, 12, 12, 27, 40, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 27, 27, 40, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/127 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506675285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506675285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675285 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 16, 16, 16, 16, 16, 16, 16, 32, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 16, 16, 16, 16, 16, 16, 32, 32, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506675285 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285 Building ZINC000506675285 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506675285 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 126) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506675285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506675285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675285 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 12, 12, 12, 12, 12, 12, 12, 27, 40, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 27, 27, 40, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 127) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O) `ZINC000506675285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506675285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675285 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 16, 16, 16, 16, 16, 16, 16, 32, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 16, 16, 16, 16, 16, 16, 32, 32, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506675285 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675285 Building ZINC000506675286 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506675286 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/128 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506675286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506675286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675286 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 17, 17, 17, 17, 17, 17, 17, 33, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 17, 17, 17, 17, 17, 17, 33, 33, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/129 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506675286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506675286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675286 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 12, 12, 12, 12, 12, 12, 12, 26, 41, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 26, 26, 41, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506675286 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286 Building ZINC000506675286 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506675286 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 128) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506675286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506675286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675286 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 17, 17, 17, 17, 17, 17, 17, 33, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 17, 17, 17, 17, 17, 17, 33, 33, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 129) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O) `ZINC000506675286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506675286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000506675286 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 12, 12, 12, 12, 12, 12, 12, 26, 41, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 26, 26, 41, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506675286 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506675286 Building ZINC000506685512 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506685512 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/130 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@H]2CNS(C)(=O)=O)cn1) `ZINC000506685512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506685512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685512 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 15, 31, 32, 32, 32, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 9, 9, 9, 9, 9, 9, 15, 15, 31, 32, 32, 32, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/131 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@H]2CNS(C)(=O)=O)cn1) `ZINC000506685512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506685512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685512 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 13, 34, 37, 37, 37, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 7, 7, 7, 7, 7, 7, 13, 13, 34, 37, 37, 37, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506685512 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512 Building ZINC000506685512 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506685512 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 130) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@H]2CNS(C)(=O)=O)cn1) `ZINC000506685512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506685512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685512 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 15, 31, 32, 32, 32, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 9, 9, 9, 9, 9, 9, 15, 15, 31, 32, 32, 32, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 131) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@H]2CNS(C)(=O)=O)cn1) `ZINC000506685512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506685512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685512 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 13, 34, 37, 37, 37, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 7, 7, 7, 7, 7, 7, 13, 13, 34, 37, 37, 37, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506685512 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685512 Building ZINC000506685513 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506685513 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/132 `/scratch/xiaobo/316102/xbz-8058115.52/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)N[C@@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1) `ZINC000506685513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506685513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685513 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 8, 12, 37, 38, 38, 38, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 8, 8, 8, 8, 8, 8, 12, 12, 37, 38, 38, 38, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/133 `/scratch/xiaobo/316102/xbz-8058115.52/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)N[C@@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1) `ZINC000506685513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506685513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685513 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 9, 9, 9, 9, 9, 9, 9, 14, 32, 32, 32, 32, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 9, 9, 9, 9, 9, 9, 14, 14, 32, 32, 32, 32, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506685513 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513 Building ZINC000506685513 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506685513 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 132) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)N[C@@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1) `ZINC000506685513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506685513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685513 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 8, 12, 37, 38, 38, 38, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 8, 8, 8, 8, 8, 8, 12, 12, 37, 38, 38, 38, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 133) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)N[C@@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1) `ZINC000506685513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506685513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685513 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 9, 9, 9, 9, 9, 9, 9, 14, 32, 32, 32, 32, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 9, 9, 9, 9, 9, 9, 14, 14, 32, 32, 32, 32, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506685513 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685513 Building ZINC000506685514 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506685514 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/134 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCC[C@H]2CNS(C)(=O)=O)cn1) `ZINC000506685514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506685514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685514 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCC[C@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 10, 10, 10, 10, 10, 10, 10, 16, 33, 35, 35, 35, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 10, 10, 10, 10, 10, 10, 16, 16, 33, 35, 35, 35, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/135 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCC[C@H]2CNS(C)(=O)=O)cn1) `ZINC000506685514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506685514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685514 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCC[C@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 15, 29, 29, 29, 29, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 11, 11, 11, 11, 11, 11, 15, 15, 29, 29, 29, 29, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506685514 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514 Building ZINC000506685514 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506685514 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 134) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCC[C@H]2CNS(C)(=O)=O)cn1) `ZINC000506685514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506685514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685514 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCC[C@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 10, 10, 10, 10, 10, 10, 10, 16, 33, 35, 35, 35, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 10, 10, 10, 10, 10, 10, 16, 16, 33, 35, 35, 35, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 135) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCC[C@H]2CNS(C)(=O)=O)cn1) `ZINC000506685514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506685514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685514 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCC[C@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 15, 29, 29, 29, 29, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 11, 11, 11, 11, 11, 11, 15, 15, 29, 29, 29, 29, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506685514 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685514 Building ZINC000506685515 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506685515 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/136 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1) `ZINC000506685515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506685515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685515 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 15, 29, 29, 29, 29, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 10, 10, 10, 10, 10, 10, 15, 15, 29, 29, 29, 29, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/137 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1) `ZINC000506685515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506685515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685515 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 15, 32, 33, 33, 33, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 10, 10, 10, 10, 10, 10, 15, 15, 32, 33, 33, 33, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506685515 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515 Building ZINC000506685515 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506685515 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 136) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1) `ZINC000506685515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506685515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685515 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 15, 29, 29, 29, 29, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 10, 10, 10, 10, 10, 10, 15, 15, 29, 29, 29, 29, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 137) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1) `ZINC000506685515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506685515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000506685515 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCC[C@@H]2CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 15, 32, 33, 33, 33, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 10, 10, 10, 10, 10, 10, 15, 15, 32, 33, 33, 33, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000506685515 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000506685515 Building ZINC001520796621 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520796621 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/138 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)COCc2nccn2C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001520796621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520796621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001520796621 none C[C@@H]1[C@@H](NC(=O)COCc2nccn2C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 8, 26, 32, 49, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 26, 26, 49, 49, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/139 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)COCc2nccn2C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001520796621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520796621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001520796621 none C[C@@H]1[C@@H](NC(=O)COCc2nccn2C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 41, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 22, 22, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53] set([32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 39, 38, 31]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520796621 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621 Building ZINC001520796621 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520796621 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 138) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)COCc2nccn2C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001520796621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520796621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001520796621 none C[C@@H]1[C@@H](NC(=O)COCc2nccn2C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 8, 26, 32, 49, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 26, 26, 49, 49, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 139) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)COCc2nccn2C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001520796621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520796621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001520796621 none C[C@@H]1[C@@H](NC(=O)COCc2nccn2C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 41, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 22, 22, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53] set([32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 39, 38, 31]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520796621 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520796621 Building ZINC001701217182 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701217182 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/140 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701217182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701217182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001701217182 none C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 19, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 48, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/141 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701217182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701217182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001701217182 none C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 24, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 24, 44, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701217182 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182 Building ZINC001701217182 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701217182 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 140) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701217182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701217182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001701217182 none C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 19, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 48, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 141) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701217182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701217182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001701217182 none C[C@@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 24, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 24, 44, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701217182 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217182 Building ZINC001701217183 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701217183 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/142 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701217183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701217183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001701217183 none C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 22, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 41, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/143 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701217183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701217183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001701217183 none C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 23, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 45, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701217183 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183 Building ZINC001701217183 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701217183 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 142) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701217183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701217183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001701217183 none C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 22, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 41, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 143) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701217183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701217183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001701217183 none C[C@H](CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 23, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 45, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701217183 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701217183 Building ZINC000855015146 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855015146 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/144 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@]1(C)C[C@]1(F)Cl) `ZINC000855015146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855015146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000855015146 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@]1(C)C[C@]1(F)Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 4, 1, 1, 1, 1, 2, 2, 2, 12, 16, 19, 19, 19, 19, 19, 4, 4, 4, 4, 8, 8, 4, 2, 12, 12, 16, 16, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/145 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@]1(C)C[C@]1(F)Cl) `ZINC000855015146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855015146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000855015146 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@]1(C)C[C@]1(F)Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 2, 1, 1, 1, 1, 2, 2, 2, 11, 15, 19, 19, 19, 19, 19, 2, 2, 2, 2, 5, 5, 2, 2, 11, 11, 15, 15, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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/316102/xbz-8058115.52/working/building/ZINC000855015146 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000855015146 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146 Building ZINC000855015146 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855015146 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 144) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@]1(C)C[C@]1(F)Cl) `ZINC000855015146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855015146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000855015146 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@]1(C)C[C@]1(F)Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 4, 1, 1, 1, 1, 2, 2, 2, 12, 16, 19, 19, 19, 19, 19, 4, 4, 4, 4, 8, 8, 4, 2, 12, 12, 16, 16, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 145) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@]1(C)C[C@]1(F)Cl) `ZINC000855015146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855015146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000855015146 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@]1(C)C[C@]1(F)Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 2, 1, 1, 1, 1, 2, 2, 2, 11, 15, 19, 19, 19, 19, 19, 2, 2, 2, 2, 5, 5, 2, 2, 11, 11, 15, 15, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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/316102/xbz-8058115.52/working/building/ZINC000855015146 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000855015146 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855015146 Building ZINC001719605141 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719605141 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/146 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001719605141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719605141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001719605141 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 128 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/147 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001719605141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719605141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001719605141 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 36, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719605141 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141 Building ZINC001719605141 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719605141 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 146) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001719605141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719605141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001719605141 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 128 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 147) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001719605141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719605141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001719605141 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 36, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719605141 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605141 Building ZINC001719605183 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719605183 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/148 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCC(=O)N(C)C) `ZINC001719605183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719605183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001719605183 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCC(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 13, 13, 27, 25, 39, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 27, 27, 32, 32, 35, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 231 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/149 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCC(=O)N(C)C) `ZINC001719605183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719605183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001719605183 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCC(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 13, 28, 26, 41, 50, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 28, 28, 32, 32, 39, 38, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 230 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719605183 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183 Building ZINC001719605183 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719605183 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 148) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCC(=O)N(C)C) `ZINC001719605183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719605183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001719605183 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCC(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 13, 13, 27, 25, 39, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 27, 27, 32, 32, 35, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 231 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 149) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCC(=O)N(C)C) `ZINC001719605183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719605183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001719605183 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCC(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 13, 28, 26, 41, 50, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 28, 28, 32, 32, 39, 38, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 230 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719605183 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605183 Building ZINC001719605191 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719605191 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/150 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc2n1CCOC2) `ZINC001719605191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719605191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001719605191 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc2n1CCOC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 21, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/151 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc2n1CCOC2) `ZINC001719605191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719605191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001719605191 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc2n1CCOC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719605191 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191 Building ZINC001719605191 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719605191 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 150) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc2n1CCOC2) `ZINC001719605191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719605191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001719605191 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc2n1CCOC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 21, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 151) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc2n1CCOC2) `ZINC001719605191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719605191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001719605191 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cnc2n1CCOC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719605191 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719605191 Building ZINC001701242173 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701242173 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/152 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001701242173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701242173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001701242173 none CC[C@@H]1CCO[C@@H]1C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 43, 43, 43, 43, 43, 43, 20, 43, 9, 20, 9, 9, 4, 9, 14, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 46, 46, 46, 46, 46, 43, 43, 43, 43, 9, 9, 14, 14, 19, 19, 57, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 263 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/153 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001701242173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701242173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001701242173 none CC[C@@H]1CCO[C@@H]1C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 47, 47, 47, 47, 47, 47, 18, 47, 4, 18, 4, 4, 4, 4, 6, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 49, 49, 49, 49, 49, 47, 47, 47, 47, 4, 4, 6, 6, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 206 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701242173 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173 Building ZINC001701242173 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701242173 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 152) grep: /scratch/xiaobo/316102/xbz-8058115.52/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@@H]1CCO[C@@H]1C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001701242173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701242173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001701242173 none CC[C@@H]1CCO[C@@H]1C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 43, 43, 43, 43, 43, 43, 20, 43, 9, 20, 9, 9, 4, 9, 14, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 46, 46, 46, 46, 46, 43, 43, 43, 43, 9, 9, 14, 14, 19, 19, 57, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 263 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 153) grep: /scratch/xiaobo/316102/xbz-8058115.52/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@@H]1CCO[C@@H]1C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001701242173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701242173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001701242173 none CC[C@@H]1CCO[C@@H]1C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 47, 47, 47, 47, 47, 47, 18, 47, 4, 18, 4, 4, 4, 4, 6, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 49, 49, 49, 49, 49, 47, 47, 47, 47, 4, 4, 6, 6, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 206 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701242173 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701242173 Building ZINC001719606278 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719606278 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/154 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CNC(=O)c1ccoc1) `ZINC001719606278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719606278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001719606278 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CNC(=O)c1ccoc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 26, 40, 40, 40, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 26, 26, 40, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/155 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CNC(=O)c1ccoc1) `ZINC001719606278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719606278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001719606278 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CNC(=O)c1ccoc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 26, 34, 34, 34, 50, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 34, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719606278 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278 Building ZINC001719606278 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719606278 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 154) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CNC(=O)c1ccoc1) `ZINC001719606278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719606278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001719606278 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CNC(=O)c1ccoc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 26, 40, 40, 40, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 26, 26, 40, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 155) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CNC(=O)c1ccoc1) `ZINC001719606278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719606278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001719606278 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CNC(=O)c1ccoc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 26, 34, 34, 34, 50, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 34, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719606278 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606278 Building ZINC001719606422 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719606422 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/156 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCCN(C(N)=O)C1) `ZINC001719606422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719606422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001719606422 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 19, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/157 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCCN(C(N)=O)C1) `ZINC001719606422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719606422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001719606422 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 18, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719606422 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422 Building ZINC001719606422 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719606422 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 156) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCCN(C(N)=O)C1) `ZINC001719606422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719606422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001719606422 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 19, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 157) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCCN(C(N)=O)C1) `ZINC001719606422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719606422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001719606422 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 18, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719606422 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719606422 Building ZINC001280903150 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001280903150 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/158 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001280903150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001280903150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001280903150 none CN(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 35, 26, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 35, 35, 26, 26, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 8, 41, 10, 11, 12, 13, 14, 15, 48, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 203 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/159 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001280903150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001280903150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001280903150 none CN(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 30, 22, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 39, 39, 30, 30, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 8, 41, 10, 11, 12, 13, 14, 15, 48, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 201 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001280903150 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150 Building ZINC001280903150 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001280903150 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 158) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001280903150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001280903150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001280903150 none CN(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 35, 26, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 35, 35, 26, 26, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 8, 41, 10, 11, 12, 13, 14, 15, 48, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 203 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 159) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001280903150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001280903150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001280903150 none CN(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 30, 22, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 39, 39, 30, 30, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 8, 41, 10, 11, 12, 13, 14, 15, 48, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 201 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001280903150 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280903150 Building ZINC000410167065 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000410167065 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/160 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 5, 6, 8, 9, 24, 24, 24, 24, 24, 22, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 10, 10, 8, 8, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 22, 24, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/161 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 5, 6, 8, 9, 24, 24, 24, 24, 24, 22, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 10, 10, 8, 8, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 22, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/162 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/162' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 5, 6, 8, 9, 24, 24, 24, 24, 24, 24, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 24, 24, 24, 10, 10, 8, 8, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 2, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/163 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/163' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 5, 4, 5, 7, 8, 21, 21, 21, 21, 21, 20, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 9, 9, 7, 7, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000410167065 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 Building ZINC000410167065 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000410167065 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 160) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 5, 6, 8, 9, 24, 24, 24, 24, 24, 22, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 10, 10, 8, 8, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 22, 24, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 161) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 5, 6, 8, 9, 24, 24, 24, 24, 24, 22, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 10, 10, 8, 8, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 22, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 162) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 5, 6, 8, 9, 24, 24, 24, 24, 24, 24, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 24, 24, 24, 10, 10, 8, 8, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 2, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 163) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 5, 4, 5, 7, 8, 21, 21, 21, 21, 21, 20, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 9, 9, 7, 7, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000410167065 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 Building ZINC000410167065 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000410167065 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 160) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 5, 6, 8, 9, 24, 24, 24, 24, 24, 22, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 10, 10, 8, 8, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 22, 24, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 161) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 5, 6, 8, 9, 24, 24, 24, 24, 24, 22, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 10, 10, 8, 8, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 22, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 162) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 5, 6, 8, 9, 24, 24, 24, 24, 24, 24, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 24, 24, 24, 10, 10, 8, 8, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 2, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 163) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 5, 4, 5, 7, 8, 21, 21, 21, 21, 21, 20, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 9, 9, 7, 7, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000410167065 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 Building ZINC000410167065 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000410167065 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 160) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 5, 6, 8, 9, 24, 24, 24, 24, 24, 22, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 10, 10, 8, 8, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 22, 24, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 161) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 5, 6, 8, 9, 24, 24, 24, 24, 24, 22, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 10, 10, 8, 8, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 22, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 162) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 5, 6, 8, 9, 24, 24, 24, 24, 24, 24, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 24, 24, 24, 10, 10, 8, 8, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 2, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 163) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000410167065.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000410167065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410167065 none COC(=O)CN(CC[N@]1CC[N@@](C)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 5, 10, 5, 5, 10, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 5, 4, 5, 7, 8, 21, 21, 21, 21, 21, 20, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 9, 9, 7, 7, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000410167065 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000410167065 Building ZINC000552417775 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000552417775 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/164 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(O)CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000552417775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000552417775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000552417775 none O=C(NCC1(O)CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 17, 17, 87, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/165 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(O)CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000552417775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000552417775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000552417775 none O=C(NCC1(O)CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 14, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 14, 14, 69, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000552417775 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775 Building ZINC000552417775 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000552417775 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 164) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(NCC1(O)CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000552417775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000552417775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000552417775 none O=C(NCC1(O)CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 17, 17, 87, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 165) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(NCC1(O)CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000552417775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000552417775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000552417775 none O=C(NCC1(O)CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 14, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 14, 14, 69, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000552417775 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552417775 Building ZINC000242836124 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242836124 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/166 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)c(F)c1F)N1CCN(C2CC2)CC1) `ZINC000242836124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242836124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242836124 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)c(F)c1F)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 15, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 43, 45, 45, 45, 45, 45, 45, 45, 45, 18, 18, 5, 4, 4, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 137 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/167 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)c(F)c1F)N1CCN(C2CC2)CC1) `ZINC000242836124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242836124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242836124 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)c(F)c1F)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 15, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 17, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 43, 44, 44, 44, 44, 44, 44, 44, 44, 17, 17, 5, 4, 4, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242836124 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124 Building ZINC000242836124 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242836124 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 166) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)c(F)c1F)N1CCN(C2CC2)CC1) `ZINC000242836124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242836124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242836124 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)c(F)c1F)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 15, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 43, 45, 45, 45, 45, 45, 45, 45, 45, 18, 18, 5, 4, 4, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 137 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 167) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)c(F)c1F)N1CCN(C2CC2)CC1) `ZINC000242836124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242836124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242836124 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)c(F)c1F)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 15, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 17, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 43, 44, 44, 44, 44, 44, 44, 44, 44, 17, 17, 5, 4, 4, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242836124 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242836124 Building ZINC000507705347 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000507705347 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/168 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/168' -> `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)S(N)(=O)=O) `ZINC000507705347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000507705347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000507705347 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)S(N)(=O)=O NO_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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 30, 30, 30, 39, 39, 39, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 4, 17, 17, 30, 30, 30, 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]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/169 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/169' -> `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)S(N)(=O)=O) `ZINC000507705347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000507705347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000507705347 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)S(N)(=O)=O NO_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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 4, 4, 4, 16, 32, 32, 32, 44, 44, 44, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 4, 16, 16, 32, 32, 32, 44, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000507705347 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347 Building ZINC000507705347 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000507705347 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 168) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)S(N)(=O)=O) `ZINC000507705347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000507705347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000507705347 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)S(N)(=O)=O NO_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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 30, 30, 30, 39, 39, 39, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 4, 17, 17, 30, 30, 30, 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]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 169) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)S(N)(=O)=O) `ZINC000507705347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000507705347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000507705347 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)S(N)(=O)=O NO_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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 4, 4, 4, 16, 32, 32, 32, 44, 44, 44, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 4, 16, 16, 32, 32, 32, 44, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000507705347 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705347 Building ZINC000507705352 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000507705352 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/170 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/170' -> `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)S(N)(=O)=O) `ZINC000507705352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000507705352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000507705352 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)S(N)(=O)=O NO_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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 5, 5, 5, 19, 32, 32, 32, 44, 44, 44, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 5, 19, 19, 32, 32, 32, 44, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/171 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/171' -> `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)S(N)(=O)=O) `ZINC000507705352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000507705352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000507705352 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)S(N)(=O)=O NO_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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 3, 3, 3, 16, 29, 29, 29, 39, 39, 39, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 3, 16, 16, 29, 29, 29, 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]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000507705352 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352 Building ZINC000507705352 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000507705352 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 170) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)S(N)(=O)=O) `ZINC000507705352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000507705352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000507705352 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)S(N)(=O)=O NO_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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 5, 5, 5, 19, 32, 32, 32, 44, 44, 44, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 5, 19, 19, 32, 32, 32, 44, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 171) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)S(N)(=O)=O) `ZINC000507705352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000507705352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000507705352 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)S(N)(=O)=O NO_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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 3, 3, 3, 16, 29, 29, 29, 39, 39, 39, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 3, 16, 16, 29, 29, 29, 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]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000507705352 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000507705352 Building ZINC001280937633 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001280937633 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/172 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001280937633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001280937633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001280937633 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 11, 22, 24, 29, 29, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 11, 11, 24, 24, 29, 29, 29, 29, 34, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/173 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001280937633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001280937633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001280937633 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 13, 21, 27, 29, 29, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 13, 13, 27, 27, 29, 29, 29, 29, 36, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001280937633 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633 Building ZINC001280937633 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001280937633 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 172) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001280937633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001280937633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001280937633 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 11, 22, 24, 29, 29, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 11, 11, 24, 24, 29, 29, 29, 29, 34, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 173) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001280937633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001280937633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001280937633 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 13, 21, 27, 29, 29, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 13, 13, 27, 27, 29, 29, 29, 29, 36, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001280937633 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280937633 Building ZINC001280939351 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001280939351 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/174 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@H]2CC[C@@H]1O2) `ZINC001280939351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001280939351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001280939351 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@H]2CC[C@@H]1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 10, 20, 23, 28, 28, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 10, 10, 23, 23, 28, 28, 28, 28, 34, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/175 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@H]2CC[C@@H]1O2) `ZINC001280939351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001280939351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001280939351 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@H]2CC[C@@H]1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 11, 20, 25, 30, 30, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 11, 11, 25, 25, 30, 30, 30, 30, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001280939351 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351 Building ZINC001280939351 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001280939351 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 174) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@H]2CC[C@@H]1O2) `ZINC001280939351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001280939351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001280939351 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@H]2CC[C@@H]1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 10, 20, 23, 28, 28, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 10, 10, 23, 23, 28, 28, 28, 28, 34, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 175) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@H]2CC[C@@H]1O2) `ZINC001280939351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001280939351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001280939351 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCOCCCNC(=O)[C@@H]1C[C@H]2CC[C@@H]1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 11, 20, 25, 30, 30, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 11, 11, 25, 25, 30, 30, 30, 30, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001280939351 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001280939351 Building ZINC000552878087 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000552878087 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/176 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CNS(C)(=O)=O)CC2)cn1) `ZINC000552878087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000552878087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000552878087 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CNS(C)(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', '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, 5, 5, 5, 8, 14, 5, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 17, 35, 37, 37, 37, 4, 4, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 17, 17, 35, 37, 37, 37, 4, 4, 4, 4, 2] 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/177 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(CNS(C)(=O)=O)CC2)cn1) `ZINC000552878087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000552878087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000552878087 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(CNS(C)(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', '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, 5, 5, 5, 8, 14, 5, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 3, 3, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 16, 35, 41, 41, 41, 4, 4, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 4, 4, 4, 4, 4, 16, 16, 35, 41, 41, 41, 4, 4, 4, 4, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000552878087 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087 Building ZINC000552878087 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000552878087 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 176) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CNS(C)(=O)=O)CC2)cn1) `ZINC000552878087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000552878087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000552878087 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(CNS(C)(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', '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, 5, 5, 5, 8, 14, 5, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 17, 35, 37, 37, 37, 4, 4, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 17, 17, 35, 37, 37, 37, 4, 4, 4, 4, 2] 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 177) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(CNS(C)(=O)=O)CC2)cn1) `ZINC000552878087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000552878087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000552878087 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(CNS(C)(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', '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, 5, 5, 5, 8, 14, 5, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 3, 3, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 16, 35, 41, 41, 41, 4, 4, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 4, 4, 4, 4, 4, 16, 16, 35, 41, 41, 41, 4, 4, 4, 4, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000552878087 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000552878087 Building ZINC001520863748 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520863748 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/178 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCCS(C)(=O)=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001520863748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520863748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520863748 none C[C@@H]1[C@@H](NC(=O)CCCS(C)(=O)=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 9, 9, 9, 38, 25, 42, 50, 50, 50, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 38, 38, 38, 38, 41, 39, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 280 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/179 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCCS(C)(=O)=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001520863748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520863748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520863748 none C[C@@H]1[C@@H](NC(=O)CCCS(C)(=O)=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 10, 10, 10, 40, 33, 43, 50, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 40, 40, 42, 42, 43, 43, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520863748 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748 Building ZINC001520863748 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520863748 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 178) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)CCCS(C)(=O)=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001520863748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520863748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520863748 none C[C@@H]1[C@@H](NC(=O)CCCS(C)(=O)=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 9, 9, 9, 38, 25, 42, 50, 50, 50, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 38, 38, 38, 38, 41, 39, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 280 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 179) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)CCCS(C)(=O)=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001520863748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520863748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520863748 none C[C@@H]1[C@@H](NC(=O)CCCS(C)(=O)=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 10, 10, 10, 40, 33, 43, 50, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 40, 40, 42, 42, 43, 43, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520863748 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520863748 Building ZINC000242925660 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242925660 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/180 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)N1CCN(C2CC2)CC1) `ZINC000242925660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242925660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242925660 none O=C(CNC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 24, 30, 30, 30, 30, 31, 31, 30, 30, 8, 8, 3, 4, 4, 7, 7, 7, 7, 7, 30, 30, 30, 30, 31, 31, 31, 31, 31, 30, 30, 30, 30] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/181 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)N1CCN(C2CC2)CC1) `ZINC000242925660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242925660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242925660 none O=C(CNC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 31, 31, 31, 31, 32, 32, 31, 31, 9, 9, 3, 4, 4, 8, 8, 8, 8, 8, 31, 31, 31, 31, 32, 32, 32, 32, 32, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242925660 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660 Building ZINC000242925660 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242925660 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 180) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)N1CCN(C2CC2)CC1) `ZINC000242925660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242925660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242925660 none O=C(CNC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 24, 30, 30, 30, 30, 31, 31, 30, 30, 8, 8, 3, 4, 4, 7, 7, 7, 7, 7, 30, 30, 30, 30, 31, 31, 31, 31, 31, 30, 30, 30, 30] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 181) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)N1CCN(C2CC2)CC1) `ZINC000242925660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242925660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242925660 none O=C(CNC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 31, 31, 31, 31, 32, 32, 31, 31, 9, 9, 3, 4, 4, 8, 8, 8, 8, 8, 31, 31, 31, 31, 32, 32, 32, 32, 32, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242925660 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242925660 Building ZINC001342809419 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001342809419 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/182 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 36, 36, 36, 36, 16, 36, 11, 16, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 11, 36, 50, 50, 50, 50, 50, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11, 36, 36] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/183 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 41, 41, 41, 15, 41, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 15, 10, 41, 50, 50, 50, 50, 50, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 41, 41] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/184 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/184' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 46, 46, 46, 22, 46, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 18, 12, 46, 50, 50, 50, 50, 50, 46, 46, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 12, 12, 46, 46] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/185 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/185' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 39, 39, 39, 17, 39, 12, 17, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 17, 12, 39, 50, 50, 50, 50, 50, 39, 39, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 12, 12, 39, 39] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342809419 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 Building ZINC001342809419 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001342809419 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 182) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 36, 36, 36, 36, 16, 36, 11, 16, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 11, 36, 50, 50, 50, 50, 50, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11, 36, 36] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 183) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 41, 41, 41, 15, 41, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 15, 10, 41, 50, 50, 50, 50, 50, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 41, 41] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 184) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 46, 46, 46, 22, 46, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 18, 12, 46, 50, 50, 50, 50, 50, 46, 46, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 12, 12, 46, 46] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 185) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 39, 39, 39, 17, 39, 12, 17, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 17, 12, 39, 50, 50, 50, 50, 50, 39, 39, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 12, 12, 39, 39] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342809419 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 Building ZINC001342809419 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001342809419 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 182) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 36, 36, 36, 36, 16, 36, 11, 16, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 11, 36, 50, 50, 50, 50, 50, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11, 36, 36] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 183) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 41, 41, 41, 15, 41, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 15, 10, 41, 50, 50, 50, 50, 50, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 41, 41] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 184) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 46, 46, 46, 22, 46, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 18, 12, 46, 50, 50, 50, 50, 50, 46, 46, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 12, 12, 46, 46] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 185) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 39, 39, 39, 17, 39, 12, 17, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 17, 12, 39, 50, 50, 50, 50, 50, 39, 39, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 12, 12, 39, 39] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342809419 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 Building ZINC001342809419 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001342809419 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 182) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 36, 36, 36, 36, 16, 36, 11, 16, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 11, 36, 50, 50, 50, 50, 50, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11, 36, 36] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 183) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 41, 41, 41, 15, 41, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 15, 10, 41, 50, 50, 50, 50, 50, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 41, 41] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 184) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 46, 46, 46, 22, 46, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 18, 12, 46, 50, 50, 50, 50, 50, 46, 46, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 12, 12, 46, 46] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 185) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1) `ZINC001342809419.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001342809419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342809419 none CCO[C@H]1C[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 39, 39, 39, 17, 39, 12, 17, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 17, 12, 39, 50, 50, 50, 50, 50, 39, 39, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 12, 12, 39, 39] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342809419 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809419 Building ZINC001342809653 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342809653 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/186 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H](NC(C)=O)C(C)C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342809653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342809653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001342809653 none CO[C@@H]1CN(C(=O)[C@H](NC(C)=O)C(C)C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 5, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 9, 9, 9, 21, 21, 42, 42, 48, 48, 48, 42, 50, 49, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 9, 9, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/187 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H](NC(C)=O)C(C)C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342809653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342809653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001342809653 none CO[C@@H]1CN(C(=O)[C@H](NC(C)=O)C(C)C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 5, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 10, 10, 10, 21, 21, 41, 41, 46, 46, 46, 41, 50, 49, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10, 46, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342809653 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653 Building ZINC001342809653 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342809653 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 186) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@H](NC(C)=O)C(C)C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342809653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342809653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001342809653 none CO[C@@H]1CN(C(=O)[C@H](NC(C)=O)C(C)C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 5, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 9, 9, 9, 21, 21, 42, 42, 48, 48, 48, 42, 50, 49, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 9, 9, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 187) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@H](NC(C)=O)C(C)C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342809653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342809653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001342809653 none CO[C@@H]1CN(C(=O)[C@H](NC(C)=O)C(C)C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 8, 1, 5, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 10, 10, 10, 21, 21, 41, 41, 46, 46, 46, 41, 50, 49, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10, 46, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342809653 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342809653 Building ZINC001342810032 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342810032 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/188 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)n1) `ZINC001342810032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001342810032 none COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 8, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 48, 19, 10, 19, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 14, 10, 48, 50, 50, 50, 48, 48, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/189 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)n1) `ZINC001342810032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001342810032 none COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 8, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 19, 11, 19, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 11, 47, 50, 50, 50, 47, 47, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342810032 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032 Building ZINC001342810032 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342810032 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 188) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)n1) `ZINC001342810032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001342810032 none COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 8, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 48, 19, 10, 19, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 14, 10, 48, 50, 50, 50, 48, 48, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 189) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)n1) `ZINC001342810032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001342810032 none COc1nccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 8, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 19, 11, 19, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 11, 47, 50, 50, 50, 47, 47, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342810032 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810032 Building ZINC001342810068 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342810068 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/190 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1OCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001342810068 none CC[C@@H]1OCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 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, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 42, 42, 42, 42, 21, 42, 11, 21, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 11, 50, 50, 50, 50, 50, 42, 42, 42, 42, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/191 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1OCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001342810068 none CC[C@@H]1OCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 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, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 45, 45, 45, 45, 23, 45, 12, 23, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 18, 12, 50, 50, 50, 50, 50, 45, 45, 45, 45, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 12, 12] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342810068 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068 Building ZINC001342810068 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342810068 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 190) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1OCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001342810068 none CC[C@@H]1OCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 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, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 42, 42, 42, 42, 21, 42, 11, 21, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 11, 50, 50, 50, 50, 50, 42, 42, 42, 42, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 191) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1OCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001342810068 none CC[C@@H]1OCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 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, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 45, 45, 45, 45, 23, 45, 12, 23, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 18, 12, 50, 50, 50, 50, 50, 45, 45, 45, 45, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 12, 12] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342810068 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810068 Building ZINC001342810850 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342810850 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/192 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001342810850 none CCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 37, 16, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 9, 50, 50, 50, 50, 50, 37, 37, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 9, 9] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/193 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001342810850 none CCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 35, 35, 19, 10, 19, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 15, 10, 50, 50, 50, 50, 50, 35, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342810850 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850 Building ZINC001342810850 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342810850 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 192) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001342810850 none CCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 37, 16, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 9, 50, 50, 50, 50, 50, 37, 37, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 9, 9] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 193) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342810850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001342810850 none CCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 35, 35, 19, 10, 19, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 15, 10, 50, 50, 50, 50, 50, 35, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342810850 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342810850 Building ZINC001342812044 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342812044 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/194 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342812044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342812044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001342812044 none CCNC(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 44, 35, 44, 20, 20, 7, 5, 7, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 5, 50, 50, 50, 50, 50, 44, 31, 32, 24, 24, 20, 20, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 5, 5] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/195 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342812044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342812044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001342812044 none CCNC(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 35, 41, 20, 22, 8, 6, 8, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 6, 50, 50, 50, 50, 50, 41, 31, 33, 25, 25, 22, 22, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342812044 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044 Building ZINC001342812044 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342812044 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 194) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342812044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342812044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001342812044 none CCNC(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 44, 35, 44, 20, 20, 7, 5, 7, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 5, 50, 50, 50, 50, 50, 44, 31, 32, 24, 24, 20, 20, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 5, 5] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 195) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001342812044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342812044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001342812044 none CCNC(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 35, 41, 20, 22, 8, 6, 8, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 6, 50, 50, 50, 50, 50, 41, 31, 33, 25, 25, 22, 22, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342812044 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812044 Building ZINC001342812206 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342812206 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/196 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2nn(C)cc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342812206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342812206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001342812206 none CO[C@@H]1CN(C(=O)c2nn(C)cc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 13, 13, 13, 13, 13, 26, 26, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/197 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2nn(C)cc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342812206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342812206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001342812206 none CO[C@@H]1CN(C(=O)c2nn(C)cc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 12, 12, 12, 25, 25, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342812206 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206 Building ZINC001342812206 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342812206 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 196) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2nn(C)cc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342812206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342812206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001342812206 none CO[C@@H]1CN(C(=O)c2nn(C)cc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 13, 13, 13, 13, 13, 26, 26, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 197) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2nn(C)cc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342812206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342812206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001342812206 none CO[C@@H]1CN(C(=O)c2nn(C)cc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 12, 12, 12, 25, 25, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342812206 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812206 Building ZINC001342812269 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342812269 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/198 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CC2(OC)CCC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342812269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342812269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001342812269 none CO[C@@H]1CN(C(=O)CC2(OC)CCC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 11, 11, 11, 11, 11, 19, 19, 41, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/199 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CC2(OC)CCC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342812269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342812269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001342812269 none CO[C@@H]1CN(C(=O)CC2(OC)CCC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 10, 10, 10, 10, 10, 17, 17, 40, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342812269 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269 Building ZINC001342812269 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342812269 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 198) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CC2(OC)CCC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342812269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342812269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001342812269 none CO[C@@H]1CN(C(=O)CC2(OC)CCC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 11, 11, 11, 11, 11, 19, 19, 41, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 199) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CC2(OC)CCC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342812269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342812269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001342812269 none CO[C@@H]1CN(C(=O)CC2(OC)CCC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 10, 10, 10, 10, 10, 17, 17, 40, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342812269 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342812269 Building ZINC000242962535 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242962535 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/200 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)c(F)c1)N1CCN(C2CC2)CC1) `ZINC000242962535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242962535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242962535 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)c(F)c1)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 23, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 4, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/201 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)c(F)c1)N1CCN(C2CC2)CC1) `ZINC000242962535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242962535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242962535 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)c(F)c1)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 4, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242962535 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535 Building ZINC000242962535 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000242962535 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 200) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)c(F)c1)N1CCN(C2CC2)CC1) `ZINC000242962535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000242962535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242962535 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)c(F)c1)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 23, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 4, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 201) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)c(F)c1)N1CCN(C2CC2)CC1) `ZINC000242962535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000242962535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000242962535 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)c(F)c1)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 4, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000242962535 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000242962535 Building ZINC000648550373 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648550373 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/202 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC000648550373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648550373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000648550373 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 13, 20, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/203 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC000648550373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648550373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000648550373 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 2, 12, 17, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000648550373 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373 Building ZINC000648550373 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648550373 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 202) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC000648550373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648550373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000648550373 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 13, 20, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 203) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC000648550373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648550373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000648550373 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 2, 12, 17, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000648550373 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550373 Building ZINC000648550374 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648550374 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/204 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC000648550374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648550374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000648550374 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 24, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/205 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC000648550374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648550374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000648550374 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 9, 20, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 43, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000648550374 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374 Building ZINC000648550374 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648550374 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 204) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC000648550374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648550374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000648550374 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 24, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 205) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC000648550374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648550374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000648550374 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 9, 20, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 43, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000648550374 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648550374 Building ZINC000648623831 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648623831 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/206 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@]1(C(F)(F)F)CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000648623831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648623831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000648623831 none CNC(=O)[C@]1(C(F)(F)F)CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 27, 11, 11, 11, 11, 11, 11, 11, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 27, 27, 27, 27, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/207 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@]1(C(F)(F)F)CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000648623831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648623831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000648623831 none CNC(=O)[C@]1(C(F)(F)F)CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 13, 13, 13, 13, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 13, 26, 26, 26, 26, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 64 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000648623831 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831 Building ZINC000648623831 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648623831 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 206) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)[C@]1(C(F)(F)F)CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000648623831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648623831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000648623831 none CNC(=O)[C@]1(C(F)(F)F)CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 27, 11, 11, 11, 11, 11, 11, 11, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 27, 27, 27, 27, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 207) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)[C@]1(C(F)(F)F)CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000648623831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648623831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000648623831 none CNC(=O)[C@]1(C(F)(F)F)CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 13, 13, 13, 13, 13, 13, 13, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 13, 26, 26, 26, 26, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 64 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000648623831 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623831 Building ZINC000648623832 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648623832 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/208 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@]1(C(F)(F)F)CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000648623832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648623832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000648623832 none CNC(=O)[C@@]1(C(F)(F)F)CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 26, 12, 12, 12, 12, 12, 12, 12, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 26, 26, 26, 26, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/209 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@]1(C(F)(F)F)CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000648623832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648623832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000648623832 none CNC(=O)[C@@]1(C(F)(F)F)CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 29, 12, 12, 12, 12, 12, 12, 12, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 29, 29, 29, 29, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000648623832 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832 Building ZINC000648623832 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648623832 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 208) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)[C@@]1(C(F)(F)F)CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000648623832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648623832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000648623832 none CNC(=O)[C@@]1(C(F)(F)F)CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 26, 12, 12, 12, 12, 12, 12, 12, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 26, 26, 26, 26, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 209) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)[C@@]1(C(F)(F)F)CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000648623832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648623832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000648623832 none CNC(=O)[C@@]1(C(F)(F)F)CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 29, 12, 12, 12, 12, 12, 12, 12, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 29, 29, 29, 29, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000648623832 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000648623832 Building ZINC000508197867 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508197867 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/210 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1cc[nH]n1) `ZINC000508197867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508197867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000508197867 none O=C(NCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1cc[nH]n1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 6, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 44, 50, 50, 50, 50, 50, 44, 22, 22, 12, 12, 2, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/211 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1cc[nH]n1) `ZINC000508197867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508197867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000508197867 none O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1cc[nH]n1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 6, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 44, 50, 50, 50, 50, 50, 44, 22, 22, 12, 12, 2, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000508197867 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867 Building ZINC000508197867 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508197867 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 210) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1cc[nH]n1) `ZINC000508197867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508197867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000508197867 none O=C(NCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1cc[nH]n1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 6, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 44, 50, 50, 50, 50, 50, 44, 22, 22, 12, 12, 2, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 211) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1cc[nH]n1) `ZINC000508197867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508197867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000508197867 none O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1cc[nH]n1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 6, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 44, 50, 50, 50, 50, 50, 44, 22, 22, 12, 12, 2, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000508197867 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000508197867 Building ZINC000243052599 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243052599 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/212 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])C3CCC3)CC2)c1) `ZINC000243052599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243052599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000243052599 none COc1cccc(N2CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])C3CCC3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 19, 19, 19, 19, 16, 10, 18, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 19, 19, 35, 42, 42, 42, 35, 35, 35, 19, 19, 19, 19, 9, 9, 3, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 35] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/213 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])C3CCC3)CC2)c1) `ZINC000243052599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243052599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000243052599 none COc1cccc(N2CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])C3CCC3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 21, 21, 21, 21, 19, 10, 21, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 21, 21, 38, 40, 40, 40, 38, 38, 38, 21, 21, 21, 21, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 38] 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000243052599 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599 Building ZINC000243052599 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243052599 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 212) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cccc(N2CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])C3CCC3)CC2)c1) `ZINC000243052599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243052599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000243052599 none COc1cccc(N2CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])C3CCC3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 19, 19, 19, 19, 16, 10, 18, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 19, 19, 35, 42, 42, 42, 35, 35, 35, 19, 19, 19, 19, 9, 9, 3, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 35] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 213) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cccc(N2CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])C3CCC3)CC2)c1) `ZINC000243052599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243052599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000243052599 none COc1cccc(N2CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])C3CCC3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 21, 21, 21, 21, 19, 10, 21, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 21, 21, 38, 40, 40, 40, 38, 38, 38, 21, 21, 21, 21, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 38] 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000243052599 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243052599 Building ZINC001520903266 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520903266 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/214 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001520903266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520903266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001520903266 none C[C@@H]1[C@@H](NC(=O)[C@@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 7, 8, 1, 8, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 47, 47, 50, 50, 50, 47, 50, 50, 50, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 57, 55, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 206 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/215 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001520903266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520903266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001520903266 none C[C@@H]1[C@@H](NC(=O)[C@@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 7, 8, 1, 8, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 23, 23, 23, 47, 47, 50, 50, 50, 47, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 57, 55, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 215 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520903266 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266 Building ZINC001520903266 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520903266 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 214) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)[C@@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001520903266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520903266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001520903266 none C[C@@H]1[C@@H](NC(=O)[C@@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 7, 8, 1, 8, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 47, 47, 50, 50, 50, 47, 50, 50, 50, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 57, 55, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 206 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 215) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1[C@@H](NC(=O)[C@@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001520903266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520903266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001520903266 none C[C@@H]1[C@@H](NC(=O)[C@@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 7, 8, 1, 8, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 23, 23, 23, 47, 47, 50, 50, 50, 47, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 57, 55, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 215 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520903266 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903266 Building ZINC001520903283 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520903283 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/216 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001520903283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520903283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001520903283 none C[C@@H]1[C@@H](NC(=O)[C@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 7, 8, 1, 8, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 57, 55, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/217 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001520903283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520903283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001520903283 none C[C@@H]1[C@@H](NC(=O)[C@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 7, 8, 1, 8, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 57, 55, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520903283 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283 Building ZINC001520903283 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520903283 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 216) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001520903283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520903283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001520903283 none C[C@@H]1[C@@H](NC(=O)[C@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 7, 8, 1, 8, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 57, 55, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 217) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001520903283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520903283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001520903283 none C[C@@H]1[C@@H](NC(=O)[C@H](NC(N)=O)C(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 7, 8, 1, 8, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 57, 55, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001520903283 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001520903283 Building ZINC001701359134 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701359134 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/218 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1[C@H]2CN(C(=O)[C@H]3CC[C@@H](C(N)=O)C3)C[C@H]21) `ZINC001701359134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701359134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001701359134 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1[C@H]2CN(C(=O)[C@H]3CC[C@@H](C(N)=O)C3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 23, 23, 23, 23, 23, 23, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/219 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1[C@H]2CN(C(=O)[C@H]3CC[C@@H](C(N)=O)C3)C[C@H]21) `ZINC001701359134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701359134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001701359134 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1[C@H]2CN(C(=O)[C@H]3CC[C@@H](C(N)=O)C3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 24, 24, 24, 24, 24, 24, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701359134 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134 Building ZINC001701359134 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701359134 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 218) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1[C@H]2CN(C(=O)[C@H]3CC[C@@H](C(N)=O)C3)C[C@H]21) `ZINC001701359134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701359134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001701359134 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1[C@H]2CN(C(=O)[C@H]3CC[C@@H](C(N)=O)C3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 23, 23, 23, 23, 23, 23, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 219) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1[C@H]2CN(C(=O)[C@H]3CC[C@@H](C(N)=O)C3)C[C@H]21) `ZINC001701359134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701359134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001701359134 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1[C@H]2CN(C(=O)[C@H]3CC[C@@H](C(N)=O)C3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 24, 24, 24, 24, 24, 24, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701359134 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701359134 Building ZINC000553629045 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000553629045 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/220 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 4, 4, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/221 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 15, 15, 7, 7, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/222 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/222' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 4, 4, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/223 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/223' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 15, 15, 7, 7, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000553629045 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 Building ZINC000553629045 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000553629045 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 220) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 4, 4, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 221) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 15, 15, 7, 7, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 222) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 4, 4, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 223) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 15, 15, 7, 7, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000553629045 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 Building ZINC000553629045 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000553629045 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 220) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 4, 4, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 221) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 15, 15, 7, 7, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 222) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 4, 4, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 223) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 15, 15, 7, 7, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000553629045 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 Building ZINC000553629045 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000553629045 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 220) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 4, 4, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 221) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 15, 15, 7, 7, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 222) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 4, 4, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 223) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1) `ZINC000553629045.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000553629045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000553629045 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2CCC3(CC2)NC(=O)NC3=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 15, 15, 7, 7, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000553629045 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553629045 Building ZINC000605096478 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605096478 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/224 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1) `ZINC000605096478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605096478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000605096478 none Cn1cc(N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 11, 11, 11, 11, 7, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/225 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1) `ZINC000605096478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605096478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000605096478 none Cn1cc(N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 10, 10, 10, 10, 6, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 10, 10, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000605096478 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478 Building ZINC000605096478 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605096478 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 224) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1) `ZINC000605096478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605096478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000605096478 none Cn1cc(N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 11, 11, 11, 11, 7, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 225) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1) `ZINC000605096478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605096478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000605096478 none Cn1cc(N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 10, 10, 10, 10, 6, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 10, 10, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000605096478 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096478 Building ZINC000605096479 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605096479 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/226 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1) `ZINC000605096479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605096479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000605096479 none Cn1cc(N2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 12, 12, 12, 12, 7, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 12, 12, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/227 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1) `ZINC000605096479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605096479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000605096479 none Cn1cc(N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 10, 10, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000605096479 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479 Building ZINC000605096479 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605096479 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 226) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(N2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1) `ZINC000605096479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605096479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000605096479 none Cn1cc(N2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 12, 12, 12, 12, 7, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 12, 12, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 227) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1) `ZINC000605096479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605096479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000605096479 none Cn1cc(N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 10, 10, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000605096479 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000605096479 Building ZINC000243071641 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243071641 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/228 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2F)CC1) `ZINC000243071641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243071641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000243071641 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 18, 23, 23, 23, 23, 32, 32, 32, 32, 32, 32, 23, 23, 10, 10, 4, 4, 4, 4, 4, 23, 23, 23, 23, 32, 32, 32, 32, 23, 23, 23, 23] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/229 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2F)CC1) `ZINC000243071641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243071641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000243071641 none O=C(CNC(=O)[C@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 17, 23, 23, 23, 23, 31, 31, 31, 31, 31, 31, 23, 23, 10, 10, 4, 4, 4, 4, 4, 23, 23, 23, 23, 31, 31, 31, 31, 23, 23, 23, 23] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 88 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000243071641 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641 Building ZINC000243071641 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243071641 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 228) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2F)CC1) `ZINC000243071641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243071641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000243071641 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 18, 23, 23, 23, 23, 32, 32, 32, 32, 32, 32, 23, 23, 10, 10, 4, 4, 4, 4, 4, 23, 23, 23, 23, 32, 32, 32, 32, 23, 23, 23, 23] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 229) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2F)CC1) `ZINC000243071641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243071641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000243071641 none O=C(CNC(=O)[C@]([O-])([SiH3])c1cccnc1)N1CCN(c2ccccc2F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 17, 23, 23, 23, 23, 31, 31, 31, 31, 31, 31, 23, 23, 10, 10, 4, 4, 4, 4, 4, 23, 23, 23, 23, 31, 31, 31, 31, 23, 23, 23, 23] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 88 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000243071641 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243071641 Building ZINC000553811651 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553811651 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/230 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)N(C)C)C1) `ZINC000553811651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553811651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000553811651 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 30, 30, 30, 30, 30, 30, 50, 50, 50, 50, 50, 30, 3, 3, 3, 3, 3, 3, 3, 4, 30, 30, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/231 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)N(C)C)C1) `ZINC000553811651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553811651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000553811651 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 26, 26, 26, 26, 26, 26, 47, 47, 47, 49, 49, 26, 3, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 26, 26, 49, 49, 49, 49, 49, 49, 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]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000553811651 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651 Building ZINC000553811651 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553811651 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 230) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)N(C)C)C1) `ZINC000553811651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553811651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000553811651 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 30, 30, 30, 30, 30, 30, 50, 50, 50, 50, 50, 30, 3, 3, 3, 3, 3, 3, 3, 4, 30, 30, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 231) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)N(C)C)C1) `ZINC000553811651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553811651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000553811651 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 26, 26, 26, 26, 26, 26, 47, 47, 47, 49, 49, 26, 3, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 26, 26, 49, 49, 49, 49, 49, 49, 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]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000553811651 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000553811651 Building ZINC000485621384 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485621384 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/232 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@H]1COCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485621384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621384 none COCCO[C@H]1COCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 21, 13, 8, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 28, 28, 28, 23, 23, 21, 21, 8, 8, 8, 8, 8, 8, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/233 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@H]1COCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485621384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621384 none COCCO[C@H]1COCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 24, 14, 9, 9, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 34, 34, 34, 27, 27, 24, 24, 9, 9, 9, 9, 9, 9, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000485621384 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384 Building ZINC000485621384 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485621384 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 232) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCO[C@H]1COCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485621384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621384 none COCCO[C@H]1COCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 21, 13, 8, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 28, 28, 28, 23, 23, 21, 21, 8, 8, 8, 8, 8, 8, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 233) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCO[C@H]1COCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485621384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621384 none COCCO[C@H]1COCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 24, 14, 9, 9, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 34, 34, 34, 27, 27, 24, 24, 9, 9, 9, 9, 9, 9, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000485621384 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621384 Building ZINC000485621386 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485621386 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/234 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@H]1COCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485621386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621386 none COCCO[C@H]1COCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 33, 29, 14, 10, 10, 10, 10, 10, 10, 10, 5, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 39, 39, 39, 33, 33, 29, 29, 10, 10, 10, 10, 10, 10, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/235 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@H]1COCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485621386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621386 none COCCO[C@H]1COCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 24, 14, 10, 10, 10, 10, 10, 10, 10, 5, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 29, 29, 29, 27, 27, 24, 24, 10, 10, 10, 10, 10, 10, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000485621386 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386 Building ZINC000485621386 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485621386 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 234) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCO[C@H]1COCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485621386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621386 none COCCO[C@H]1COCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 33, 29, 14, 10, 10, 10, 10, 10, 10, 10, 5, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 39, 39, 39, 33, 33, 29, 29, 10, 10, 10, 10, 10, 10, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 235) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCO[C@H]1COCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485621386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621386 none COCCO[C@H]1COCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 24, 14, 10, 10, 10, 10, 10, 10, 10, 5, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 29, 29, 29, 27, 27, 24, 24, 10, 10, 10, 10, 10, 10, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000485621386 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621386 Building ZINC000485621387 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485621387 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/236 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@@H]1COCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485621387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621387 none COCCO[C@@H]1COCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 24, 13, 9, 9, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 28, 28, 28, 27, 27, 24, 24, 9, 9, 9, 9, 9, 9, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/237 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@@H]1COCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485621387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621387 none COCCO[C@@H]1COCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 29, 25, 13, 8, 8, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 35, 35, 35, 29, 29, 25, 25, 8, 8, 8, 8, 8, 8, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000485621387 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387 Building ZINC000485621387 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485621387 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 236) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCO[C@@H]1COCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485621387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621387 none COCCO[C@@H]1COCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 24, 13, 9, 9, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 28, 28, 28, 27, 27, 24, 24, 9, 9, 9, 9, 9, 9, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 237) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCO[C@@H]1COCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485621387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621387 none COCCO[C@@H]1COCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 29, 25, 13, 8, 8, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 35, 35, 35, 29, 29, 25, 25, 8, 8, 8, 8, 8, 8, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000485621387 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621387 Building ZINC000485621389 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485621389 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/238 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@@H]1COCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485621389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621389 none COCCO[C@@H]1COCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 27, 25, 14, 8, 8, 8, 8, 8, 8, 8, 5, 8, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 5, 35, 35, 35, 27, 27, 25, 25, 8, 8, 8, 8, 8, 8, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/239 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@@H]1COCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485621389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621389 none COCCO[C@@H]1COCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 30, 26, 13, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 35, 35, 35, 30, 30, 26, 26, 7, 7, 7, 7, 7, 7, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/316102/xbz-8058115.52/working/building/ZINC000485621389 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000485621389 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389 Building ZINC000485621389 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485621389 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 238) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCO[C@@H]1COCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485621389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621389 none COCCO[C@@H]1COCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 27, 25, 14, 8, 8, 8, 8, 8, 8, 8, 5, 8, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 5, 35, 35, 35, 27, 27, 25, 25, 8, 8, 8, 8, 8, 8, 2, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 239) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCO[C@@H]1COCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000485621389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485621389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000485621389 none COCCO[C@@H]1COCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 30, 26, 13, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 35, 35, 35, 30, 30, 26, 26, 7, 7, 7, 7, 7, 7, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/316102/xbz-8058115.52/working/building/ZINC000485621389 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000485621389 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000485621389 Building ZINC001342889663 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342889663 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/240 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@H](C)n1ccnc1) `ZINC001342889663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342889663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342889663 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@H](C)n1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 5, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 11, 20, 29, 29, 29, 50, 50, 50, 50, 11, 11, 11, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 11, 20, 20, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/241 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@H](C)n1ccnc1) `ZINC001342889663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342889663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342889663 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@H](C)n1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 18, 27, 27, 27, 50, 50, 50, 50, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 18, 18, 27, 27, 27, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342889663 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663 Building ZINC001342889663 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342889663 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 240) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@H](C)n1ccnc1) `ZINC001342889663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342889663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342889663 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@H](C)n1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 5, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 11, 20, 29, 29, 29, 50, 50, 50, 50, 11, 11, 11, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 11, 20, 20, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 241) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@H](C)n1ccnc1) `ZINC001342889663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342889663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342889663 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@H](C)n1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 18, 27, 27, 27, 50, 50, 50, 50, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 18, 18, 27, 27, 27, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342889663 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889663 Building ZINC001342889664 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342889664 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/242 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@@H](C)n1ccnc1) `ZINC001342889664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342889664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342889664 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@@H](C)n1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 11, 11, 11, 22, 32, 32, 32, 50, 50, 50, 50, 12, 12, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 11, 22, 22, 32, 32, 32, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/243 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@@H](C)n1ccnc1) `ZINC001342889664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342889664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342889664 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@@H](C)n1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 18, 29, 29, 29, 50, 50, 50, 50, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 18, 18, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342889664 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664 Building ZINC001342889664 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342889664 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 242) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@@H](C)n1ccnc1) `ZINC001342889664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342889664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342889664 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@@H](C)n1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 11, 11, 11, 22, 32, 32, 32, 50, 50, 50, 50, 12, 12, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 11, 22, 22, 32, 32, 32, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 243) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@@H](C)n1ccnc1) `ZINC001342889664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342889664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342889664 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C[C@@H](C)n1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 18, 29, 29, 29, 50, 50, 50, 50, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 18, 18, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342889664 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342889664 Building ZINC000554295818 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000554295818 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/244 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CS(N)(=O)=O)C2)cn1) `ZINC000554295818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000554295818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000554295818 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CS(N)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 4, 4, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 17, 28, 28, 28, 6, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 17, 17, 28, 28, 6, 6, 4] 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]) total number of confs: 142 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/245 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CS(N)(=O)=O)C2)cn1) `ZINC000554295818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000554295818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000554295818 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CS(N)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 9, 11, 11, 11, 11, 11, 11, 20, 36, 36, 36, 11, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 11, 11, 11, 11, 11, 11, 20, 20, 36, 36, 11, 11, 5] 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]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000554295818 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818 Building ZINC000554295818 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000554295818 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 244) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CS(N)(=O)=O)C2)cn1) `ZINC000554295818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000554295818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000554295818 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CS(N)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 4, 4, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 17, 28, 28, 28, 6, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 17, 17, 28, 28, 6, 6, 4] 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]) total number of confs: 142 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 245) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CS(N)(=O)=O)C2)cn1) `ZINC000554295818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000554295818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000554295818 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CS(N)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 9, 11, 11, 11, 11, 11, 11, 20, 36, 36, 36, 11, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 11, 11, 11, 11, 11, 11, 20, 20, 36, 36, 11, 11, 5] 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]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000554295818 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295818 Building ZINC000554295819 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000554295819 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/246 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CS(N)(=O)=O)C2)cn1) `ZINC000554295819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000554295819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000554295819 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CS(N)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 2, 6, 9, 11, 11, 11, 11, 11, 11, 19, 36, 36, 36, 11, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 11, 11, 11, 11, 11, 11, 19, 19, 36, 36, 11, 11, 5] 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]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/247 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CS(N)(=O)=O)C2)cn1) `ZINC000554295819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000554295819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000554295819 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CS(N)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 2, 3, 4, 7, 7, 7, 7, 7, 7, 16, 30, 30, 30, 7, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 7, 7, 7, 7, 7, 7, 16, 16, 30, 30, 7, 7, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000554295819 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819 Building ZINC000554295819 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000554295819 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 246) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CS(N)(=O)=O)C2)cn1) `ZINC000554295819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000554295819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000554295819 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CS(N)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 2, 6, 9, 11, 11, 11, 11, 11, 11, 19, 36, 36, 36, 11, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 11, 11, 11, 11, 11, 11, 19, 19, 36, 36, 11, 11, 5] 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]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 247) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CS(N)(=O)=O)C2)cn1) `ZINC000554295819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000554295819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000554295819 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CS(N)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 2, 3, 4, 7, 7, 7, 7, 7, 7, 16, 30, 30, 30, 7, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 7, 7, 7, 7, 7, 7, 16, 16, 30, 30, 7, 7, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000554295819 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000554295819 Building ZINC001342903111 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342903111 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/248 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1) `ZINC001342903111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342903111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342903111 none CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 13, 33, 13, 13, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 33, 47, 47, 38, 38, 38, 38, 38, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 47, 47, 47, 47, 47] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/249 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1) `ZINC001342903111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342903111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342903111 none CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 15, 35, 15, 15, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 35, 50, 50, 36, 36, 36, 36, 36, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342903111 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111 Building ZINC001342903111 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342903111 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 248) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1) `ZINC001342903111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342903111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342903111 none CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 13, 33, 13, 13, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 33, 47, 47, 38, 38, 38, 38, 38, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 47, 47, 47, 47, 47] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 249) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1) `ZINC001342903111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342903111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342903111 none CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 15, 35, 15, 15, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 35, 50, 50, 36, 36, 36, 36, 36, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342903111 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903111 Building ZINC001342903112 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342903112 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/250 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1) `ZINC001342903112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342903112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342903112 none CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 16, 44, 16, 16, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 44, 49, 49, 45, 45, 45, 45, 45, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 49, 49, 49, 49, 49] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/251 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1) `ZINC001342903112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342903112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342903112 none CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 15, 38, 15, 15, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 38, 48, 48, 42, 42, 42, 42, 42, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 48, 48, 48, 48, 48] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342903112 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112 Building ZINC001342903112 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342903112 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 250) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1) `ZINC001342903112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342903112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342903112 none CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 16, 44, 16, 16, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 44, 49, 49, 45, 45, 45, 45, 45, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 49, 49, 49, 49, 49] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 251) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1) `ZINC001342903112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342903112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342903112 none CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 15, 38, 15, 15, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 38, 48, 48, 42, 42, 42, 42, 42, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 48, 48, 48, 48, 48] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342903112 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342903112 Building ZINC000472053803 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000472053803 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/252 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000472053803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000472053803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000472053803 none COC(=O)C[C@@H](C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 33, 13, 4, 13, 13, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 4, 4, 33, 33, 33, 14, 14, 13, 13, 13, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 119 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/253 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](C)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000472053803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000472053803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000472053803 none COC(=O)C[C@@H](C)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 33, 13, 4, 13, 13, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 33, 33, 33, 14, 14, 13, 13, 13, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000472053803 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803 Building ZINC000472053803 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000472053803 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 252) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)C[C@@H](C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000472053803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000472053803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000472053803 none COC(=O)C[C@@H](C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 33, 13, 4, 13, 13, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 4, 4, 33, 33, 33, 14, 14, 13, 13, 13, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 119 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 253) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)C[C@@H](C)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000472053803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000472053803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000472053803 none COC(=O)C[C@@H](C)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 33, 13, 4, 13, 13, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 33, 33, 33, 14, 14, 13, 13, 13, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000472053803 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000472053803 Building ZINC000486090924 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486090924 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/254 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)C(=O)[C@H]1CSCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000486090924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486090924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000486090924 none CN(Cc1ccco1)C(=O)[C@H]1CSCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 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, 6, 16, 27, 28, 28, 28, 28, 3, 6, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 16, 27, 27, 28, 28, 28, 3, 3, 3, 3, 2, 2, 2, 2, 2] 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: 107 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/255 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccco1)C(=O)[C@H]1CSCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000486090924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486090924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000486090924 none CN(Cc1ccco1)C(=O)[C@H]1CSCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 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: [14, 5, 14, 27, 31, 31, 31, 31, 2, 5, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 14, 14, 14, 27, 27, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000486090924 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924 Building ZINC000486090924 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000486090924 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 254) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(Cc1ccco1)C(=O)[C@H]1CSCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000486090924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000486090924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000486090924 none CN(Cc1ccco1)C(=O)[C@H]1CSCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 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, 6, 16, 27, 28, 28, 28, 28, 3, 6, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 16, 27, 27, 28, 28, 28, 3, 3, 3, 3, 2, 2, 2, 2, 2] 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: 107 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 255) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(Cc1ccco1)C(=O)[C@H]1CSCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000486090924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000486090924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000486090924 none CN(Cc1ccco1)C(=O)[C@H]1CSCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 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: [14, 5, 14, 27, 31, 31, 31, 31, 2, 5, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 14, 14, 14, 27, 27, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000486090924 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000486090924 Building ZINC001118721358 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118721358 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/256 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H]2[C@@H](C1)C2(F)F) `ZINC001118721358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118721358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001118721358 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H]2[C@@H](C1)C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 5, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 16, 16, 5, 4, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/257 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H]2[C@@H](C1)C2(F)F) `ZINC001118721358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118721358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001118721358 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H]2[C@@H](C1)C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 5, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 16, 16, 5, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 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/316102/xbz-8058115.52/working/building/ZINC001118721358 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001118721358 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358 Building ZINC001118721358 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118721358 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 256) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H]2[C@@H](C1)C2(F)F) `ZINC001118721358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118721358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001118721358 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H]2[C@@H](C1)C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 5, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 16, 16, 5, 4, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 257) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H]2[C@@H](C1)C2(F)F) `ZINC001118721358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118721358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001118721358 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H]2[C@@H](C1)C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 5, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 16, 16, 5, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 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/316102/xbz-8058115.52/working/building/ZINC001118721358 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001118721358 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721358 Building ZINC001118721360 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118721360 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/258 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@@H]2[C@H](C1)C2(F)F) `ZINC001118721360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118721360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001118721360 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@@H]2[C@H](C1)C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 5, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 16, 16, 5, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/259 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@@H]2[C@H](C1)C2(F)F) `ZINC001118721360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118721360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001118721360 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@@H]2[C@H](C1)C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 5, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 16, 16, 5, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001118721360 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360 Building ZINC001118721360 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118721360 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 258) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@@H]2[C@H](C1)C2(F)F) `ZINC001118721360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118721360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001118721360 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@@H]2[C@H](C1)C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 5, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 16, 16, 5, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 259) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@@H]2[C@H](C1)C2(F)F) `ZINC001118721360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118721360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001118721360 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@@H]2[C@H](C1)C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 5, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 16, 16, 5, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001118721360 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118721360 Building ZINC000194315914 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194315914 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/260 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc2ccc(N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)nn12) `ZINC000194315914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194315914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000194315914 none Cc1nnc2ccc(N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)nn12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 9, 2, 10, 1, 1, 1, 3, 3, 1, 3, 3, 22, 22, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 3, 3, 1, 3, 3, 22, 22, 22, 22] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 90 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/261 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc2ccc(N3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)nn12) `ZINC000194315914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194315914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000194315914 none Cc1nnc2ccc(N3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)nn12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 19, 19, 19, 19, 6, 2, 9, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 3, 3, 1, 3, 3, 19, 19, 19, 19] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000194315914 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914 Building ZINC000194315914 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194315914 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 260) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nnc2ccc(N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)nn12) `ZINC000194315914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194315914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000194315914 none Cc1nnc2ccc(N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)nn12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 9, 2, 10, 1, 1, 1, 3, 3, 1, 3, 3, 22, 22, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 3, 3, 1, 3, 3, 22, 22, 22, 22] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 90 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 261) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nnc2ccc(N3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)nn12) `ZINC000194315914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194315914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000194315914 none Cc1nnc2ccc(N3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)nn12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 19, 19, 19, 19, 6, 2, 9, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 3, 3, 1, 3, 3, 19, 19, 19, 19] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000194315914 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000194315914 Building ZINC001342954329 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342954329 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/262 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1) `ZINC001342954329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342954329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342954329 none CCOCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 33, 10, 10, 10, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 33, 33, 50, 50, 50, 50, 50, 48, 48, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 33, 33, 33, 33] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/263 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1) `ZINC001342954329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342954329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342954329 none CCOCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 35, 13, 13, 13, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 35, 35, 50, 50, 50, 50, 50, 50, 50, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 35, 35, 35, 35] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342954329 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329 Building ZINC001342954329 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342954329 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 262) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1) `ZINC001342954329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342954329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342954329 none CCOCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 33, 10, 10, 10, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 33, 33, 50, 50, 50, 50, 50, 48, 48, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 33, 33, 33, 33] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 263) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1) `ZINC001342954329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342954329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342954329 none CCOCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 35, 13, 13, 13, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 35, 35, 50, 50, 50, 50, 50, 50, 50, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 35, 35, 35, 35] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342954329 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342954329 Building ZINC000649075759 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000649075759 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/264 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000649075759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000649075759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000649075759 none C[C@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 7, 1, 11, 8, 5, 5, 10, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 20, 26, 36, 36, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 20, 20, 26, 26, 36, 36, 36, 36, 36, 36, 4, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/265 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000649075759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000649075759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000649075759 none C[C@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 7, 1, 11, 8, 5, 5, 10, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 15, 24, 32, 32, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 2, 2, 2, 15, 15, 24, 24, 32, 32, 32, 32, 32, 32, 2, 2, 4, 5, 5, 5, 5, 5, 4] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000649075759 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759 Building ZINC000649075759 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000649075759 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 264) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000649075759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000649075759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000649075759 none C[C@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 7, 1, 11, 8, 5, 5, 10, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 20, 26, 36, 36, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 20, 20, 26, 26, 36, 36, 36, 36, 36, 36, 4, 4, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 265) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000649075759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000649075759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000649075759 none C[C@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 7, 1, 11, 8, 5, 5, 10, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 15, 24, 32, 32, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 2, 2, 2, 15, 15, 24, 24, 32, 32, 32, 32, 32, 32, 2, 2, 4, 5, 5, 5, 5, 5, 4] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000649075759 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075759 Building ZINC000649075760 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000649075760 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/266 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000649075760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000649075760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000649075760 none C[C@@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 7, 1, 11, 8, 5, 5, 10, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 15, 24, 31, 31, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 2, 2, 2, 15, 15, 24, 24, 31, 31, 31, 31, 31, 31, 2, 2, 4, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/267 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000649075760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000649075760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000649075760 none C[C@@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 7, 1, 11, 8, 5, 5, 10, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 22, 25, 33, 33, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 4, 4, 4, 22, 22, 25, 25, 33, 33, 33, 33, 33, 33, 4, 4, 4, 5, 5, 5, 5, 5, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000649075760 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760 Building ZINC000649075760 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000649075760 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 266) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000649075760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000649075760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000649075760 none C[C@@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 7, 1, 11, 8, 5, 5, 10, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 15, 24, 31, 31, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 2, 2, 2, 15, 15, 24, 24, 31, 31, 31, 31, 31, 31, 2, 2, 4, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 267) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000649075760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000649075760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000649075760 none C[C@@H]1C(=O)N(CCN(C)C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 7, 1, 11, 8, 5, 5, 10, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 22, 25, 33, 33, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 4, 4, 4, 22, 22, 25, 25, 33, 33, 33, 33, 33, 33, 4, 4, 4, 5, 5, 5, 5, 5, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000649075760 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000649075760 Building ZINC001281099047 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281099047 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/268 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281099047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281099047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281099047 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 3, 6, 7, 7, 7, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 6, 6, 7, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/269 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281099047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281099047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281099047 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 7, 6, 11, 11, 11, 11, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 21, 11, 11, 11, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281099047 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047 Building ZINC001281099047 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281099047 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 268) grep: /scratch/xiaobo/316102/xbz-8058115.52/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@@]([O-])([SiH3])C(=O)N[C@@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281099047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281099047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281099047 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 3, 6, 7, 7, 7, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 6, 6, 7, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 269) grep: /scratch/xiaobo/316102/xbz-8058115.52/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@]([O-])([SiH3])C(=O)N[C@@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281099047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281099047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281099047 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 7, 6, 11, 11, 11, 11, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 21, 11, 11, 11, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281099047 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099047 Building ZINC001281099048 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281099048 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/270 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281099048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281099048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281099048 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 9, 9, 9, 9, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 15, 9, 9, 9, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/271 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281099048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281099048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281099048 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 7, 7, 7, 42, 42, 42, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 6, 6, 7, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281099048 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048 Building ZINC001281099048 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281099048 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 270) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281099048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281099048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281099048 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 9, 9, 9, 9, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 15, 9, 9, 9, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 271) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281099048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281099048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281099048 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CO)CNC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 7, 7, 7, 42, 42, 42, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 6, 6, 7, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281099048 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281099048 Building ZINC001342973809 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342973809 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/272 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(C)(C)CNC(C)=O) `ZINC001342973809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342973809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342973809 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(C)(C)CNC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 13, 13, 16, 16, 16, 42, 50, 50, 50, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 16, 16, 16, 16, 16, 16, 42, 42, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/273 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(C)(C)CNC(C)=O) `ZINC001342973809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342973809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342973809 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(C)(C)CNC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 13, 13, 19, 19, 19, 41, 50, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 19, 19, 19, 19, 19, 19, 41, 41, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342973809 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809 Building ZINC001342973809 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342973809 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 272) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(C)(C)CNC(C)=O) `ZINC001342973809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342973809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342973809 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(C)(C)CNC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 13, 13, 16, 16, 16, 42, 50, 50, 50, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 16, 16, 16, 16, 16, 16, 42, 42, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 273) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(C)(C)CNC(C)=O) `ZINC001342973809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342973809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342973809 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(C)(C)CNC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 13, 13, 19, 19, 19, 41, 50, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 19, 19, 19, 19, 19, 19, 41, 41, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342973809 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342973809 Building ZINC001118793199 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118793199 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/274 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1) `ZINC001118793199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118793199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001118793199 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 12, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations 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, 5, 2, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 16, 16, 16, 16, 9, 9, 2, 2, 2, 2, 5, 5, 2, 9, 9, 9, 9, 9, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/275 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1) `ZINC001118793199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118793199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001118793199 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 12, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations 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, 5, 2, 1, 1, 1, 1, 4, 8, 11, 11, 11, 11, 26, 26, 26, 26, 11, 11, 2, 2, 2, 2, 5, 5, 2, 11, 11, 11, 11, 11, 26, 26, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001118793199 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199 Building ZINC001118793199 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118793199 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 274) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1) `ZINC001118793199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118793199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001118793199 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 12, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations 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, 5, 2, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 16, 16, 16, 16, 9, 9, 2, 2, 2, 2, 5, 5, 2, 9, 9, 9, 9, 9, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 275) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1) `ZINC001118793199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118793199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001118793199 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 12, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations 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, 5, 2, 1, 1, 1, 1, 4, 8, 11, 11, 11, 11, 26, 26, 26, 26, 11, 11, 2, 2, 2, 2, 5, 5, 2, 11, 11, 11, 11, 11, 26, 26, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001118793199 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001118793199 Building ZINC001342983959 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342983959 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/276 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccon1) `ZINC001342983959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342983959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342983959 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 38, 45, 50, 50, 50, 50, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 38, 38, 45, 45, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/277 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccon1) `ZINC001342983959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342983959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342983959 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 13, 13, 13, 6, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 24, 24, 24, 45, 47, 50, 50, 50, 50, 16, 16, 16, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 24, 45, 45, 47, 47, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342983959 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959 Building ZINC001342983959 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342983959 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 276) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccon1) `ZINC001342983959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342983959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342983959 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 38, 45, 50, 50, 50, 50, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 38, 38, 45, 45, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 277) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccon1) `ZINC001342983959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342983959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342983959 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 13, 13, 13, 6, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 24, 24, 24, 45, 47, 50, 50, 50, 50, 16, 16, 16, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 24, 45, 45, 47, 47, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342983959 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342983959 Building ZINC001342987051 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342987051 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/278 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COCC(F)F) `ZINC001342987051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342987051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342987051 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 18, 35, 49, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 18, 18, 49, 49, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/279 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COCC(F)F) `ZINC001342987051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342987051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342987051 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 13, 30, 48, 50, 50, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 13, 13, 48, 48, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342987051 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051 Building ZINC001342987051 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342987051 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 278) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COCC(F)F) `ZINC001342987051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342987051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342987051 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 18, 35, 49, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 18, 18, 49, 49, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 279) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COCC(F)F) `ZINC001342987051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342987051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001342987051 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 13, 30, 48, 50, 50, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 13, 13, 48, 48, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001342987051 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001342987051 Building ZINC000412281189 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000412281189 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/280 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2cc[nH]n2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000412281189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412281189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000412281189 none O=C(N1CCN(S(=O)(=O)c2cc[nH]n2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 8, 6, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 18, 18, 18, 18, 31, 31, 31, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 18, 50, 50, 18, 18, 18, 18, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/281 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2cc[nH]n2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000412281189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412281189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000412281189 none O=C(N1CCN(S(=O)(=O)c2cc[nH]n2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 8, 6, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 31, 31, 31, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1] 50 rigid atoms, others: [1, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000412281189 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189 Building ZINC000412281189 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000412281189 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 280) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(N1CCN(S(=O)(=O)c2cc[nH]n2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000412281189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412281189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000412281189 none O=C(N1CCN(S(=O)(=O)c2cc[nH]n2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 8, 6, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 18, 18, 18, 18, 31, 31, 31, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 18, 50, 50, 18, 18, 18, 18, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 281) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(N1CCN(S(=O)(=O)c2cc[nH]n2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000412281189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412281189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000412281189 none O=C(N1CCN(S(=O)(=O)c2cc[nH]n2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 8, 6, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 31, 31, 31, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1] 50 rigid atoms, others: [1, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000412281189 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412281189 Building ZINC000606792763 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606792763 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/282 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/282' -> `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)N1CCN(c2ccnc(N(C)C)n2)CC1) `ZINC000606792763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606792763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000606792763 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2ccnc(N(C)C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 1, 8, 5, 5, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations 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, 2, 4, 9, 10, 10, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 10, 10, 10, 10] 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: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/283 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/283' -> `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)N1CCN(c2ccnc(N(C)C)n2)CC1) `ZINC000606792763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606792763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000606792763 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2ccnc(N(C)C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 1, 8, 5, 5, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations 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, 2, 5, 9, 11, 11, 11, 11, 36, 36, 36, 36, 36, 36, 36, 36, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 36, 36, 36, 36, 36, 36, 36, 36, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000606792763 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763 Building ZINC000606792763 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606792763 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 282) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2ccnc(N(C)C)n2)CC1) `ZINC000606792763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606792763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000606792763 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2ccnc(N(C)C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 1, 8, 5, 5, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations 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, 2, 4, 9, 10, 10, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 10, 10, 10, 10] 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: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 283) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2ccnc(N(C)C)n2)CC1) `ZINC000606792763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606792763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000606792763 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2ccnc(N(C)C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 1, 8, 5, 5, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations 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, 2, 5, 9, 11, 11, 11, 11, 36, 36, 36, 36, 36, 36, 36, 36, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 36, 36, 36, 36, 36, 36, 36, 36, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000606792763 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606792763 Building ZINC000606832556 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606832556 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/284 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000606832556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606832556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000606832556 none NS(=O)(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 27, 27, 13, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 27, 27, 24, 13, 13, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/285 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000606832556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606832556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000606832556 none NS(=O)(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 33, 33, 18, 5, 5, 5, 5, 5, 5, 2, 1, 3, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 5, 33, 33, 29, 18, 18, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000606832556 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556 Building ZINC000606832556 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606832556 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 284) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: NS(=O)(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000606832556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606832556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000606832556 none NS(=O)(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 27, 27, 13, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 27, 27, 24, 13, 13, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 285) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: NS(=O)(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000606832556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606832556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000606832556 none NS(=O)(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 33, 33, 18, 5, 5, 5, 5, 5, 5, 2, 1, 3, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 5, 33, 33, 29, 18, 18, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000606832556 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832556 Building ZINC000606832557 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606832557 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/286 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000606832557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606832557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000606832557 none NS(=O)(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 35, 35, 14, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 35, 35, 31, 14, 14, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/287 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000606832557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606832557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000606832557 none NS(=O)(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 29, 32, 32, 16, 6, 6, 6, 6, 6, 6, 2, 1, 3, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 6, 32, 32, 29, 16, 16, 6, 6, 6, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000606832557 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557 Building ZINC000606832557 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000606832557 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 286) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: NS(=O)(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000606832557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000606832557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000606832557 none NS(=O)(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 35, 35, 14, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 35, 35, 31, 14, 14, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 287) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: NS(=O)(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000606832557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000606832557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000606832557 none NS(=O)(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 29, 32, 32, 16, 6, 6, 6, 6, 6, 6, 2, 1, 3, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 6, 32, 32, 29, 16, 16, 6, 6, 6, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000606832557 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000606832557 Building ZINC000243190807 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243190807 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/288 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])[C@@H]2CCCO2)CC1) `ZINC000243190807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243190807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000243190807 none Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])[C@@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 35, 36, 36, 35, 35, 35, 35, 18, 11, 28, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 35, 35, 36, 36, 36, 36, 36, 36, 36, 35, 35, 35, 35, 11, 11, 4, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35] 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: 116 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/289 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])[C@@H]2CCCO2)CC1) `ZINC000243190807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243190807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000243190807 none Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])[C@@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 48, 48, 46, 46, 46, 46, 25, 14, 37, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 46, 46, 48, 48, 48, 48, 47, 48, 48, 46, 46, 46, 46, 12, 12, 4, 2, 2, 2, 2, 2, 2, 46, 46, 46, 46] 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: 141 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000243190807 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807 Building ZINC000243190807 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243190807 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 288) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])[C@@H]2CCCO2)CC1) `ZINC000243190807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243190807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000243190807 none Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])[C@@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 35, 36, 36, 35, 35, 35, 35, 18, 11, 28, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 35, 35, 36, 36, 36, 36, 36, 36, 36, 35, 35, 35, 35, 11, 11, 4, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35] 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: 116 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 289) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])[C@@H]2CCCO2)CC1) `ZINC000243190807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243190807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000243190807 none Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])[C@@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 48, 48, 46, 46, 46, 46, 25, 14, 37, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 46, 46, 48, 48, 48, 48, 47, 48, 48, 46, 46, 46, 46, 12, 12, 4, 2, 2, 2, 2, 2, 2, 46, 46, 46, 46] 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: 141 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000243190807 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190807 Building ZINC000243190808 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243190808 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/290 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])[C@H]2CCCO2)CC1) `ZINC000243190808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243190808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000243190808 none Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])[C@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 48, 48, 47, 47, 47, 47, 25, 14, 38, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 47, 47, 48, 48, 48, 48, 47, 48, 48, 47, 47, 47, 47, 12, 12, 4, 2, 2, 2, 2, 2, 2, 47, 47, 47, 47] 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: 142 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/291 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])[C@H]2CCCO2)CC1) `ZINC000243190808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243190808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000243190808 none Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])[C@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 37, 37, 36, 36, 36, 36, 20, 13, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 36, 36, 37, 37, 37, 37, 36, 37, 37, 36, 36, 36, 36, 13, 13, 4, 3, 3, 3, 3, 3, 3, 36, 36, 36, 36] 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: 118 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000243190808 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808 Building ZINC000243190808 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243190808 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 290) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])[C@H]2CCCO2)CC1) `ZINC000243190808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243190808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000243190808 none Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])[C@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 48, 48, 47, 47, 47, 47, 25, 14, 38, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 47, 47, 48, 48, 48, 48, 47, 48, 48, 47, 47, 47, 47, 12, 12, 4, 2, 2, 2, 2, 2, 2, 47, 47, 47, 47] 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: 142 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 291) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])[C@H]2CCCO2)CC1) `ZINC000243190808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243190808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000243190808 none Cc1ccccc1N1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])[C@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 37, 37, 36, 36, 36, 36, 20, 13, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 36, 36, 37, 37, 37, 37, 36, 37, 37, 36, 36, 36, 36, 13, 13, 4, 3, 3, 3, 3, 3, 3, 36, 36, 36, 36] 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: 118 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000243190808 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243190808 Building ZINC001343013817 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343013817 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/292 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](NC(C)=O)C(C)C) `ZINC001343013817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343013817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001343013817 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](NC(C)=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 8, 1, 5, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 9, 9, 9, 5, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 31, 31, 40, 40, 40, 31, 47, 47, 15, 15, 15, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 18, 40, 40, 40, 40, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 253 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/293 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](NC(C)=O)C(C)C) `ZINC001343013817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343013817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001343013817 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](NC(C)=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 8, 1, 5, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 14, 28, 28, 40, 40, 40, 28, 45, 48, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 40, 40, 40, 40, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 298 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343013817 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817 Building ZINC001343013817 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343013817 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 292) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](NC(C)=O)C(C)C) `ZINC001343013817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343013817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001343013817 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](NC(C)=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 8, 1, 5, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 9, 9, 9, 5, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 31, 31, 40, 40, 40, 31, 47, 47, 15, 15, 15, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 18, 40, 40, 40, 40, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 253 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 293) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](NC(C)=O)C(C)C) `ZINC001343013817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343013817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001343013817 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](NC(C)=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 8, 1, 5, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 14, 28, 28, 40, 40, 40, 28, 45, 48, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 40, 40, 40, 40, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 298 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343013817 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343013817 Building ZINC001343014074 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343014074 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/294 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 35, 45, 35, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 47, 47, 45, 45, 45, 35, 35, 35, 35, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/295 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 35, 45, 35, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 47, 47, 45, 45, 45, 35, 35, 35, 35, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/296 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/296' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 33, 43, 33, 6, 6, 6, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 48, 48, 43, 43, 43, 33, 33, 33, 33, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/297 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/297' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 33, 43, 33, 6, 6, 6, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 48, 48, 43, 43, 43, 33, 33, 33, 33, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343014074 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 Building ZINC001343014074 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343014074 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 294) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 35, 45, 35, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 47, 47, 45, 45, 45, 35, 35, 35, 35, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 295) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 35, 45, 35, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 47, 47, 45, 45, 45, 35, 35, 35, 35, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 296) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 33, 43, 33, 6, 6, 6, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 48, 48, 43, 43, 43, 33, 33, 33, 33, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 297) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 33, 43, 33, 6, 6, 6, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 48, 48, 43, 43, 43, 33, 33, 33, 33, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343014074 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 Building ZINC001343014074 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343014074 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 294) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 35, 45, 35, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 47, 47, 45, 45, 45, 35, 35, 35, 35, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 295) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 35, 45, 35, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 47, 47, 45, 45, 45, 35, 35, 35, 35, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 296) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 33, 43, 33, 6, 6, 6, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 48, 48, 43, 43, 43, 33, 33, 33, 33, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 297) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 33, 43, 33, 6, 6, 6, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 48, 48, 43, 43, 43, 33, 33, 33, 33, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343014074 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 Building ZINC001343014074 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343014074 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 294) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 35, 45, 35, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 47, 47, 45, 45, 45, 35, 35, 35, 35, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 295) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 35, 45, 35, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 47, 47, 45, 45, 45, 35, 35, 35, 35, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 296) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 33, 43, 33, 6, 6, 6, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 48, 48, 43, 43, 43, 33, 33, 33, 33, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 297) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001343014074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343014074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343014074 none CCCN(C)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 33, 43, 33, 6, 6, 6, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 50, 48, 48, 43, 43, 43, 33, 33, 33, 33, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 50, 51, 49, 46, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343014074 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343014074 Building ZINC000487122951 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487122951 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/298 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CS(=O)(=O)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000487122951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487122951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000487122951 none COC(=O)[C@H]1CS(=O)(=O)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 11, 11, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 13, 27, 13, 13, 13, 13, 13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 27, 27, 27, 13, 13, 13, 13, 13, 13, 5, 7, 7, 7, 7, 7, 7, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/299 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CS(=O)(=O)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000487122951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487122951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000487122951 none COC(=O)[C@H]1CS(=O)(=O)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 11, 11, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 12, 25, 12, 12, 12, 12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000487122951 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951 Building ZINC000487122951 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487122951 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 298) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@H]1CS(=O)(=O)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000487122951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487122951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000487122951 none COC(=O)[C@H]1CS(=O)(=O)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 11, 11, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 13, 27, 13, 13, 13, 13, 13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 27, 27, 27, 13, 13, 13, 13, 13, 13, 5, 7, 7, 7, 7, 7, 7, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 299) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@H]1CS(=O)(=O)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000487122951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487122951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000487122951 none COC(=O)[C@H]1CS(=O)(=O)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 11, 11, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 12, 25, 12, 12, 12, 12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000487122951 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487122951 Building ZINC000412433223 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000412433223 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/300 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(COC)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000412433223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412433223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000412433223 none COCC(COC)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 10, 6, 10, 17, 23, 6, 6, 6, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 6, 6, 27, 27, 27, 18, 18, 10, 17, 17, 23, 23, 23, 6, 6, 6, 6, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/301 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(COC)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000412433223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412433223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000412433223 none COCC(COC)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 9, 17, 21, 6, 6, 6, 4, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 6, 6, 25, 25, 25, 18, 18, 9, 17, 17, 21, 21, 21, 6, 6, 6, 6, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000412433223 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223 Building ZINC000412433223 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000412433223 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 300) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCC(COC)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000412433223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412433223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000412433223 none COCC(COC)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 10, 6, 10, 17, 23, 6, 6, 6, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 6, 6, 27, 27, 27, 18, 18, 10, 17, 17, 23, 23, 23, 6, 6, 6, 6, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 301) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCC(COC)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000412433223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412433223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000412433223 none COCC(COC)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 9, 17, 21, 6, 6, 6, 4, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 6, 6, 25, 25, 25, 18, 18, 9, 17, 17, 21, 21, 21, 6, 6, 6, 6, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000412433223 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412433223 Building ZINC001701539512 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001701539512 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/302 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 50, 37, 46, 37, 37, 35, 27, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 35, 35, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 184 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/303 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 50, 37, 46, 37, 37, 35, 27, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 35, 35, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 184 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/304 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/304' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 39, 49, 39, 39, 35, 29, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 35, 35, 19, 19, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/305 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/305' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 39, 49, 39, 39, 35, 29, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 35, 35, 19, 19, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701539512 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 Building ZINC001701539512 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001701539512 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 302) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 50, 37, 46, 37, 37, 35, 27, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 35, 35, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 184 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 303) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 50, 37, 46, 37, 37, 35, 27, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 35, 35, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 184 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 304) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 39, 49, 39, 39, 35, 29, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 35, 35, 19, 19, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 305) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 39, 49, 39, 39, 35, 29, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 35, 35, 19, 19, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701539512 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 Building ZINC001701539512 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001701539512 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 302) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 50, 37, 46, 37, 37, 35, 27, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 35, 35, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 184 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 303) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 50, 37, 46, 37, 37, 35, 27, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 35, 35, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 184 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 304) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 39, 49, 39, 39, 35, 29, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 35, 35, 19, 19, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 305) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 39, 49, 39, 39, 35, 29, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 35, 35, 19, 19, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701539512 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 Building ZINC001701539512 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001701539512 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 302) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 50, 37, 46, 37, 37, 35, 27, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 35, 35, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 184 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 303) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 50, 37, 46, 37, 37, 35, 27, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 35, 35, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 184 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 304) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 39, 49, 39, 39, 35, 29, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 35, 35, 19, 19, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 305) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701539512.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001701539512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001701539512 none CC[C@@H]1[C@@H](C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 39, 49, 39, 39, 35, 29, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 35, 35, 19, 19, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701539512 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701539512 Building ZINC000412458288 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412458288 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/306 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/307 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/308 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/308' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/309 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/309' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000412458288 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 Building ZINC000412458288 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412458288 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 306) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[C@@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 307) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[C@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 308) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 309) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000412458288 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 Building ZINC000412458288 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412458288 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 306) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[C@@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 307) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[C@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 308) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 309) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000412458288 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 Building ZINC000412458288 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412458288 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 306) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[C@@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 307) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[C@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@](CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 308) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 309) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1) `ZINC000412458288.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412458288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000412458288 none C[N@]1CC[C@](CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)(N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000412458288 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412458288 Building ZINC000487209691 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487209691 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/310 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cnn(CCN3CCOCC3)c2)cn1) `ZINC000487209691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487209691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000487209691 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cnn(CCN3CCOCC3)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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 20, 20, 34, 34, 34, 34, 34, 7, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 7, 20, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 7, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/311 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cnn(CCN3CCOCC3)c2)cn1) `ZINC000487209691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487209691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000487209691 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cnn(CCN3CCOCC3)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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 21, 21, 33, 33, 33, 33, 33, 7, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 7, 21, 21, 21, 21, 33, 33, 33, 33, 33, 33, 33, 33, 7, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000487209691 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691 Building ZINC000487209691 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487209691 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 310) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cnn(CCN3CCOCC3)c2)cn1) `ZINC000487209691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487209691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000487209691 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cnn(CCN3CCOCC3)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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 20, 20, 34, 34, 34, 34, 34, 7, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 7, 20, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 7, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 311) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cnn(CCN3CCOCC3)c2)cn1) `ZINC000487209691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487209691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000487209691 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cnn(CCN3CCOCC3)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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 21, 21, 33, 33, 33, 33, 33, 7, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 7, 21, 21, 21, 21, 33, 33, 33, 33, 33, 33, 33, 33, 7, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000487209691 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487209691 Building ZINC001719684839 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719684839 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/312 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001719684839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719684839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001719684839 none CC[C@H](NC(C)=O)C(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 18, 37, 37, 50, 50, 50, 7, 18, 7, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 48, 48, 48, 48, 48, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/313 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001719684839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719684839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001719684839 none CC[C@H](NC(C)=O)C(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 19, 39, 39, 50, 50, 50, 7, 19, 7, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 49, 49, 49, 49, 49, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719684839 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839 Building ZINC001719684839 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719684839 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 312) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@H](NC(C)=O)C(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001719684839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719684839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001719684839 none CC[C@H](NC(C)=O)C(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 18, 37, 37, 50, 50, 50, 7, 18, 7, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 48, 48, 48, 48, 48, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 313) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@H](NC(C)=O)C(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001719684839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719684839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001719684839 none CC[C@H](NC(C)=O)C(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 19, 39, 39, 50, 50, 50, 7, 19, 7, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 49, 49, 49, 49, 49, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719684839 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719684839 Building ZINC001719703308 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719703308 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/314 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001719703308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719703308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001719703308 none Cc1ncnc(O)c1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 12, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 29, 37, 29, 29, 17, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 50, 50, 50, 50, 100, 29, 29, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 100 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/315 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001719703308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719703308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001719703308 none Cc1ncnc(O)c1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 12, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 50, 50, 50, 40, 34, 40, 34, 34, 18, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50, 100, 34, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34] 100 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719703308 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308 Building ZINC001719703308 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719703308 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 314) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ncnc(O)c1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001719703308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719703308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001719703308 none Cc1ncnc(O)c1C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 12, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 29, 37, 29, 29, 17, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 50, 50, 50, 50, 100, 29, 29, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 100 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 315) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ncnc(O)c1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001719703308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719703308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001719703308 none Cc1ncnc(O)c1C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 12, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 50, 50, 50, 40, 34, 40, 34, 34, 18, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50, 100, 34, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34] 100 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719703308 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719703308 Building ZINC001719704263 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719704263 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/316 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001719704263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719704263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001719704263 none CCC[C@@H](NC(N)=O)C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 23, 33, 33, 46, 46, 46, 22, 23, 22, 22, 13, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 22, 22, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/317 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001719704263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719704263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001719704263 none CCC[C@@H](NC(N)=O)C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 30, 37, 37, 47, 47, 47, 29, 30, 29, 29, 16, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 29, 29, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719704263 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263 Building ZINC001719704263 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719704263 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 316) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCC[C@@H](NC(N)=O)C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001719704263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719704263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001719704263 none CCC[C@@H](NC(N)=O)C(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 23, 33, 33, 46, 46, 46, 22, 23, 22, 22, 13, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 22, 22, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 317) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCC[C@@H](NC(N)=O)C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001719704263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719704263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001719704263 none CCC[C@@H](NC(N)=O)C(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 30, 37, 37, 47, 47, 47, 29, 30, 29, 29, 16, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 29, 29, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719704263 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719704263 Building ZINC001719758929 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719758929 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/318 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)C(C)(C)C(N)=O) `ZINC001719758929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719758929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001719758929 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)C(C)(C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 10, 19, 19, 19, 45, 45, 45, 50, 50, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 10, 10, 19, 45, 45, 45, 45, 45, 45, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/319 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)C(C)(C)C(N)=O) `ZINC001719758929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719758929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001719758929 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)C(C)(C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 9, 22, 22, 22, 47, 47, 47, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 9, 9, 22, 47, 47, 47, 47, 47, 47, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719758929 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929 Building ZINC001719758929 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719758929 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 318) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)C(C)(C)C(N)=O) `ZINC001719758929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719758929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001719758929 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)C(C)(C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 10, 19, 19, 19, 45, 45, 45, 50, 50, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 10, 10, 19, 45, 45, 45, 45, 45, 45, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 319) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)C(C)(C)C(N)=O) `ZINC001719758929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719758929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001719758929 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)C(C)(C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 9, 22, 22, 22, 47, 47, 47, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 9, 9, 22, 47, 47, 47, 47, 47, 47, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719758929 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719758929 Building ZINC001281254178 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281254178 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/320 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1) `ZINC001281254178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281254178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281254178 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 22, 13, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 43, 43, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 30, 30, 30, 22, 22, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 250 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/321 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1) `ZINC001281254178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281254178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281254178 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 23, 19, 9, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 46, 46, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 30, 30, 30, 23, 23, 57, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 248 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281254178 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178 Building ZINC001281254178 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281254178 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 320) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1) `ZINC001281254178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281254178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281254178 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 22, 13, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 43, 43, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 30, 30, 30, 22, 22, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 250 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 321) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1) `ZINC001281254178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281254178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281254178 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 23, 19, 9, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 46, 46, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 30, 30, 30, 23, 23, 57, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 248 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281254178 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254178 Building ZINC001281254179 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281254179 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/322 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1) `ZINC001281254179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281254179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281254179 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 26, 21, 10, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 44, 44, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 32, 32, 32, 26, 26, 63, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 262 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/323 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1) `ZINC001281254179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281254179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281254179 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 21, 14, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 42, 42, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 29, 29, 29, 21, 21, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 251 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281254179 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179 Building ZINC001281254179 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281254179 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 322) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1) `ZINC001281254179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281254179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281254179 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 26, 21, 10, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 44, 44, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 32, 32, 32, 26, 26, 63, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 262 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 323) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1) `ZINC001281254179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281254179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281254179 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 21, 14, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 42, 42, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 29, 29, 29, 21, 21, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 251 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281254179 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281254179 Building ZINC000487570993 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487570993 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/324 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CCn2cncn2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000487570993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487570993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000487570993 none O=C(N1CCN(CCn2cncn2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 7, 7, 7, 7, 7, 13, 15, 25, 25, 25, 25, 7, 7, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 7, 7, 7, 7, 13, 13, 15, 15, 25, 25, 7, 7, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/325 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CCn2cncn2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000487570993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487570993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000487570993 none O=C(N1CCN(CCn2cncn2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 8, 9, 9, 9, 9, 14, 17, 27, 27, 27, 27, 9, 9, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 9, 9, 9, 9, 14, 14, 17, 17, 27, 27, 9, 9, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000487570993 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993 Building ZINC000487570993 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487570993 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 324) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(N1CCN(CCn2cncn2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000487570993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487570993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000487570993 none O=C(N1CCN(CCn2cncn2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 7, 7, 7, 7, 7, 13, 15, 25, 25, 25, 25, 7, 7, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 7, 7, 7, 7, 13, 13, 15, 15, 25, 25, 7, 7, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 325) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(N1CCN(CCn2cncn2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000487570993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487570993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000487570993 none O=C(N1CCN(CCn2cncn2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 8, 9, 9, 9, 9, 14, 17, 27, 27, 27, 27, 9, 9, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 9, 9, 9, 9, 14, 14, 17, 17, 27, 27, 9, 9, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000487570993 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487570993 Building ZINC001281257788 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281257788 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/326 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001281257788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281257788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281257788 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 18, 14, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 27, 27, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 23, 23, 23, 18, 18, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 227 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/327 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001281257788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281257788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281257788 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 22, 17, 7, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 27, 27, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 23, 23, 23, 22, 22, 51, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 230 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281257788 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788 Building ZINC001281257788 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281257788 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 326) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001281257788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281257788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281257788 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 18, 14, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 27, 27, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 23, 23, 23, 18, 18, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 227 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 327) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001281257788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281257788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281257788 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 22, 17, 7, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 27, 27, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 23, 23, 23, 22, 22, 51, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 230 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281257788 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257788 Building ZINC001281257790 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281257790 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/328 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001281257790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281257790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281257790 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 16, 7, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 24, 24, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 48, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/329 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001281257790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281257790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281257790 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 12, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 18, 18, 18, 17, 17, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 213 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281257790 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790 Building ZINC001281257790 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281257790 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 328) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001281257790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281257790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281257790 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 16, 7, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 24, 24, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 48, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 329) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001281257790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281257790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281257790 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 12, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 18, 18, 18, 17, 17, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 213 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281257790 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281257790 Building ZINC000487573540 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487573540 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/330 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CCn3cncn3)CC2)cn1) `ZINC000487573540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487573540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000487573540 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CCn3cncn3)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 11, 15, 32, 32, 32, 32, 6, 6, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 6, 6, 11, 11, 15, 15, 32, 32, 6, 6, 6, 6, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/331 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(CCn3cncn3)CC2)cn1) `ZINC000487573540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487573540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000487573540 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(CCn3cncn3)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 11, 15, 31, 31, 31, 31, 7, 7, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 7, 7, 7, 7, 11, 11, 15, 15, 31, 31, 7, 7, 7, 7, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/316102/xbz-8058115.52/working/building/ZINC000487573540 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000487573540 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540 Building ZINC000487573540 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487573540 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 330) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CCn3cncn3)CC2)cn1) `ZINC000487573540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487573540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000487573540 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(CCn3cncn3)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 11, 15, 32, 32, 32, 32, 6, 6, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 6, 6, 11, 11, 15, 15, 32, 32, 6, 6, 6, 6, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 331) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(CCn3cncn3)CC2)cn1) `ZINC000487573540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487573540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000487573540 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(CCn3cncn3)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 11, 15, 31, 31, 31, 31, 7, 7, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 7, 7, 7, 7, 11, 11, 15, 15, 31, 31, 7, 7, 7, 7, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/316102/xbz-8058115.52/working/building/ZINC000487573540 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000487573540 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000487573540 Building ZINC001281261186 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281261186 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/332 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281261186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281261186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281261186 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 13, 9, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 25, 25, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 42, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 198 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/333 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281261186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281261186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281261186 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 20, 17, 8, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 29, 29, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 21, 21, 21, 20, 20, 51, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 214 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281261186 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186 Building ZINC001281261186 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281261186 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 332) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281261186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281261186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281261186 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 13, 9, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 25, 25, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 42, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 198 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 333) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281261186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281261186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281261186 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 20, 17, 8, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 29, 29, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 21, 21, 21, 20, 20, 51, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 214 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281261186 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261186 Building ZINC001281261187 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281261187 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/334 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281261187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281261187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281261187 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 19, 15, 7, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 26, 26, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 22, 22, 22, 19, 19, 45, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 215 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/335 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281261187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281261187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281261187 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 12, 8, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 26, 26, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 16, 16, 16, 12, 12, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 203 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281261187 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187 Building ZINC001281261187 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281261187 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 334) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281261187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281261187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281261187 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 19, 15, 7, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 26, 26, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 22, 22, 22, 19, 19, 45, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 215 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 335) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001281261187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281261187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001281261187 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 12, 8, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 26, 26, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 16, 16, 16, 12, 12, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 203 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281261187 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281261187 Building ZINC001701650671 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701650671 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/336 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701650671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701650671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701650671 none C[C@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 9, 10, 10, 22, 22, 23, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 10, 10, 10, 23, 23, 28, 28, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/337 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701650671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701650671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701650671 none C[C@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 12, 13, 13, 22, 22, 25, 37, 49, 49, 49, 49, 49, 49, 50, 50, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 12, 12, 13, 13, 13, 25, 25, 31, 31, 49, 49, 49, 49, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701650671 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671 Building ZINC001701650671 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701650671 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 336) grep: /scratch/xiaobo/316102/xbz-8058115.52/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](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701650671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701650671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701650671 none C[C@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 9, 10, 10, 22, 22, 23, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 10, 10, 10, 23, 23, 28, 28, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 337) grep: /scratch/xiaobo/316102/xbz-8058115.52/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](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701650671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701650671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701650671 none C[C@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 12, 13, 13, 22, 22, 25, 37, 49, 49, 49, 49, 49, 49, 50, 50, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 12, 12, 13, 13, 13, 25, 25, 31, 31, 49, 49, 49, 49, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701650671 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650671 Building ZINC001701650672 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701650672 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/338 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701650672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701650672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701650672 none C[C@@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 16, 24, 24, 26, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 16, 16, 16, 26, 26, 31, 31, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/339 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701650672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701650672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701650672 none C[C@@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 10, 13, 13, 21, 21, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 13, 13, 13, 22, 22, 27, 27, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701650672 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672 Building ZINC001701650672 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701650672 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 338) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701650672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701650672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701650672 none C[C@@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 16, 24, 24, 26, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 16, 16, 16, 26, 26, 31, 31, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 339) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701650672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701650672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701650672 none C[C@@H](CN(C)C(=O)CC[C@H]1CC[C@@H](C(N)=O)O1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 10, 13, 13, 21, 21, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 13, 13, 13, 22, 22, 27, 27, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 55, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701650672 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701650672 Building ZINC001281272657 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281272657 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/340 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1) `ZINC001281272657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281272657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281272657 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 8, 5, 1, 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, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 19, 13, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 23, 23, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 21, 21, 21, 19, 19, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 207 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/341 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1) `ZINC001281272657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281272657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281272657 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 8, 5, 1, 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, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 16, 13, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 22, 22, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 19, 19, 19, 16, 16, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281272657 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657 Building ZINC001281272657 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281272657 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 340) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1) `ZINC001281272657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281272657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281272657 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 8, 5, 1, 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, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 19, 13, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 23, 23, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 21, 21, 21, 19, 19, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 207 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 341) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1) `ZINC001281272657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281272657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281272657 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 8, 5, 1, 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, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 16, 13, 7, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 22, 22, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 19, 19, 19, 16, 16, 39, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281272657 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272657 Building ZINC001281272658 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281272658 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/342 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1) `ZINC001281272658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281272658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281272658 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 8, 5, 1, 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, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 19, 14, 7, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 23, 23, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 20, 20, 20, 19, 19, 42, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 203 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/343 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1) `ZINC001281272658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281272658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281272658 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 8, 5, 1, 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, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 18, 10, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 21, 21, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 19, 19, 19, 18, 18, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 203 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281272658 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658 Building ZINC001281272658 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281272658 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 342) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1) `ZINC001281272658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281272658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281272658 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 8, 5, 1, 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, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 19, 14, 7, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 23, 23, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 20, 20, 20, 19, 19, 42, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 203 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 343) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1) `ZINC001281272658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281272658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281272658 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 8, 5, 1, 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, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 18, 10, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 21, 21, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 19, 19, 19, 18, 18, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 203 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281272658 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281272658 Building ZINC001281276202 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281276202 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/344 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001281276202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281276202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281276202 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 31, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 19, 19, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 9, 11, 12, 13, 14, 15, 16, 49, 50, 51, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 232 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/345 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001281276202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281276202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281276202 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 10, 6, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 31, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 19, 19, 30, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 9, 11, 12, 13, 14, 15, 16, 49, 50, 51, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 241 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281276202 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202 Building ZINC001281276202 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281276202 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 344) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001281276202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281276202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281276202 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 31, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 19, 19, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 9, 11, 12, 13, 14, 15, 16, 49, 50, 51, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 232 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 345) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001281276202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281276202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281276202 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 10, 6, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 31, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 19, 19, 30, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 9, 11, 12, 13, 14, 15, 16, 49, 50, 51, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 241 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281276202 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276202 Building ZINC001281276209 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281276209 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/346 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001281276209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281276209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281276209 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 20, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 29, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 20, 20, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 9, 11, 12, 13, 14, 15, 16, 49, 50, 51, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 245 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/347 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001281276209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281276209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281276209 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 31, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 19, 19, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 9, 11, 12, 13, 14, 15, 16, 49, 50, 51, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 240 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281276209 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209 Building ZINC001281276209 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281276209 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 346) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001281276209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281276209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281276209 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 20, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 29, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 20, 20, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 9, 11, 12, 13, 14, 15, 16, 49, 50, 51, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 245 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 347) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001281276209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281276209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281276209 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 31, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 19, 19, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 9, 11, 12, 13, 14, 15, 16, 49, 50, 51, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 240 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281276209 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281276209 Building ZINC000510138170 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510138170 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/348 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000510138170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510138170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000510138170 none COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 21, 49, 10, 3, 10, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 10, 21, 21, 21, 49, 49, 49, 21, 21, 3, 3, 3, 3, 3, 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]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/349 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000510138170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510138170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000510138170 none COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 19, 46, 9, 3, 9, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 20, 20, 20, 46, 46, 46, 19, 19, 3, 3, 3, 3, 3, 20, 20, 20] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000510138170 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170 Building ZINC000510138170 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510138170 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 348) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000510138170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510138170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000510138170 none COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 21, 49, 10, 3, 10, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 10, 21, 21, 21, 49, 49, 49, 21, 21, 3, 3, 3, 3, 3, 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]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 349) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000510138170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510138170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000510138170 none COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 19, 46, 9, 3, 9, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 20, 20, 20, 46, 46, 46, 19, 19, 3, 3, 3, 3, 3, 20, 20, 20] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000510138170 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138170 Building ZINC000510138171 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510138171 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/350 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000510138171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510138171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000510138171 none COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 19, 46, 9, 3, 9, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 20, 20, 20, 46, 46, 46, 19, 19, 3, 3, 3, 3, 3, 20, 20, 20] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/351 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000510138171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510138171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000510138171 none COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 21, 49, 10, 3, 10, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 10, 21, 21, 21, 49, 49, 49, 21, 21, 3, 3, 3, 3, 3, 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]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000510138171 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171 Building ZINC000510138171 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510138171 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 350) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000510138171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510138171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000510138171 none COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 19, 46, 9, 3, 9, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 20, 20, 20, 46, 46, 46, 19, 19, 3, 3, 3, 3, 3, 20, 20, 20] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 351) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000510138171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510138171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000510138171 none COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 21, 49, 10, 3, 10, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 10, 21, 21, 21, 49, 49, 49, 21, 21, 3, 3, 3, 3, 3, 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]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000510138171 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510138171 Building ZINC001281286924 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281286924 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/352 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281286924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281286924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001281286924 none CC(C)N(CCN(C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 10, 10, 15, 15, 33, 38, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 15, 15, 15, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 185 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/353 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281286924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281286924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001281286924 none CC(C)N(CCN(C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 9, 9, 14, 14, 33, 37, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 189 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281286924 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924 Building ZINC001281286924 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281286924 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 352) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N(CCN(C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281286924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281286924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001281286924 none CC(C)N(CCN(C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 10, 10, 15, 15, 33, 38, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 15, 15, 15, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 185 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 353) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N(CCN(C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281286924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281286924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001281286924 none CC(C)N(CCN(C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 9, 9, 14, 14, 33, 37, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 189 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281286924 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281286924 Building ZINC000412962213 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000412962213 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/354 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1cn(CCCCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1) `ZINC000412962213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412962213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000412962213 none NC(=O)c1cn(CCCCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', '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: [8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 15, 12, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 17, 17, 15, 15, 15, 15, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/355 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1cn(CCCCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1) `ZINC000412962213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412962213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000412962213 none NC(=O)c1cn(CCCCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', '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: [8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 16, 13, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 18, 18, 16, 16, 15, 15, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000412962213 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213 Building ZINC000412962213 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000412962213 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 354) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: NC(=O)c1cn(CCCCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1) `ZINC000412962213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412962213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000412962213 none NC(=O)c1cn(CCCCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', '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: [8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 15, 12, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 17, 17, 15, 15, 15, 15, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 355) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: NC(=O)c1cn(CCCCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1) `ZINC000412962213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412962213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000412962213 none NC(=O)c1cn(CCCCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', '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: [8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 16, 13, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 18, 18, 16, 16, 15, 15, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000412962213 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000412962213 Building ZINC001281296272 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281296272 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/356 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001281296272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281296272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001281296272 none CC(C)N(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 20, 27, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 8, 44, 10, 11, 12, 13, 14, 15, 48, 49, 50, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56]) total number of confs: 183 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/357 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001281296272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281296272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001281296272 none CC(C)N(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 29, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 22, 31, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 8, 44, 10, 11, 12, 13, 14, 15, 48, 49, 50, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56]) total number of confs: 183 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281296272 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272 Building ZINC001281296272 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281296272 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 356) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001281296272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281296272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001281296272 none CC(C)N(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 20, 27, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 8, 44, 10, 11, 12, 13, 14, 15, 48, 49, 50, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56]) total number of confs: 183 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 357) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001281296272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281296272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001281296272 none CC(C)N(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 29, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 22, 31, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 8, 44, 10, 11, 12, 13, 14, 15, 48, 49, 50, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56]) total number of confs: 183 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281296272 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281296272 Building ZINC001281341582 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281341582 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/358 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 12, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/359 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/360 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/360' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 36, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/361 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/361' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281341582 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 Building ZINC001281341582 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281341582 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 358) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 12, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 359) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 360) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 36, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 361) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281341582 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 Building ZINC001281341582 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281341582 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 358) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 12, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 359) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 360) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 36, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 361) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281341582 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 Building ZINC001281341582 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281341582 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 358) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 12, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 359) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 360) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 36, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 361) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1) `ZINC001281341582.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281341582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281341582 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@@H]2OC[C@@H]3COCC[C@H]23)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281341582 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281341582 Building ZINC000608232210 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608232210 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/362 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1) `ZINC000608232210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608232210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608232210 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 8, 1, 1, 8, 8, 5, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 6, 11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 7, 11, 11, 11, 11, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/363 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1) `ZINC000608232210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608232210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608232210 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 8, 1, 1, 8, 8, 5, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 6, 11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 7, 11, 11, 11, 11, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 77 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000608232210 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210 Building ZINC000608232210 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608232210 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 362) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1) `ZINC000608232210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608232210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608232210 none C[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 8, 1, 1, 8, 8, 5, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 6, 11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 7, 11, 11, 11, 11, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 363) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1) `ZINC000608232210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608232210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608232210 none C[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 8, 1, 1, 8, 8, 5, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 6, 11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 7, 11, 11, 11, 11, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 77 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000608232210 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232210 Building ZINC000608232211 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608232211 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/364 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1) `ZINC000608232211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608232211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608232211 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 8, 1, 1, 8, 8, 5, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 6, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 8, 11, 11, 11, 11, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 96 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/365 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1) `ZINC000608232211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608232211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608232211 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 8, 1, 1, 8, 8, 5, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 6, 11, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 14, 14, 14, 9, 11, 11, 11, 11, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 85 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000608232211 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211 Building ZINC000608232211 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608232211 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 364) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1) `ZINC000608232211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608232211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608232211 none C[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 8, 1, 1, 8, 8, 5, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 6, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 8, 11, 11, 11, 11, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 96 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 365) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1) `ZINC000608232211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608232211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608232211 none C[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 8, 1, 1, 8, 8, 5, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 6, 11, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 14, 14, 14, 9, 11, 11, 11, 11, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 21, 21, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 85 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000608232211 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232211 Building ZINC000608232212 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608232212 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/366 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1) `ZINC000608232212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608232212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608232212 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 8, 1, 1, 8, 8, 5, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 12, 12, 12, 8, 11, 11, 11, 11, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 4, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 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, 50]) total number of confs: 77 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/367 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1) `ZINC000608232212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608232212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608232212 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 8, 1, 1, 8, 8, 5, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 11, 11, 11, 11, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000608232212 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212 Building ZINC000608232212 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608232212 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 366) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1) `ZINC000608232212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608232212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608232212 none C[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 8, 1, 1, 8, 8, 5, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 12, 12, 12, 8, 11, 11, 11, 11, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 4, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 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, 50]) total number of confs: 77 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 367) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1) `ZINC000608232212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608232212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000608232212 none C[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C(=O)N1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 11, 8, 1, 1, 8, 8, 5, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 11, 11, 11, 11, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000608232212 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608232212 Building ZINC000510848892 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510848892 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/368 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(CC(=O)OC)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000510848892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510848892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000510848892 none COC(=O)CN(CC(=O)OC)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 11, 12, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 5, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 15, 30, 5, 2, 5, 13, 30, 30, 30, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 15, 15, 13, 13, 30, 30, 30, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/369 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(CC(=O)OC)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000510848892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510848892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000510848892 none COC(=O)CN(CC(=O)OC)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 11, 12, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 5, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 13, 27, 5, 2, 5, 12, 32, 32, 32, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 13, 13, 12, 12, 32, 32, 32, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000510848892 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892 Building ZINC000510848892 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510848892 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 368) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CN(CC(=O)OC)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000510848892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510848892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000510848892 none COC(=O)CN(CC(=O)OC)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 11, 12, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 5, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 15, 30, 5, 2, 5, 13, 30, 30, 30, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 15, 15, 13, 13, 30, 30, 30, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 369) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CN(CC(=O)OC)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000510848892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510848892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000510848892 none COC(=O)CN(CC(=O)OC)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 11, 12, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 5, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 13, 27, 5, 2, 5, 12, 32, 32, 32, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 13, 13, 12, 12, 32, 32, 32, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000510848892 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000510848892 Building ZINC000488168904 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488168904 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/370 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488168904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168904 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 23, 23, 14, 23, 8, 14, 14, 8, 5, 8, 3, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 14, 14, 14, 8, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/371 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488168904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168904 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 26, 16, 26, 9, 16, 16, 9, 5, 9, 3, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 16, 16, 16, 9, 5, 5, 5, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488168904 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904 Building ZINC000488168904 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488168904 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 370) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488168904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168904 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 23, 23, 14, 23, 8, 14, 14, 8, 5, 8, 3, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 14, 14, 14, 8, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 371) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488168904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168904 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 26, 16, 26, 9, 16, 16, 9, 5, 9, 3, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 16, 16, 16, 9, 5, 5, 5, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488168904 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168904 Building ZINC000488168907 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488168907 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/372 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488168907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168907 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 26, 15, 26, 9, 15, 15, 9, 5, 9, 3, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 15, 15, 15, 9, 5, 5, 5, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/373 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488168907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168907 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 23, 14, 23, 8, 14, 14, 8, 5, 8, 3, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 14, 14, 14, 8, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488168907 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907 Building ZINC000488168907 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488168907 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 372) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488168907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168907 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 26, 15, 26, 9, 15, 15, 9, 5, 9, 3, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 15, 15, 15, 9, 5, 5, 5, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 373) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488168907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168907 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 23, 14, 23, 8, 14, 14, 8, 5, 8, 3, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 14, 14, 14, 8, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488168907 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168907 Building ZINC000488168909 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488168909 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/374 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488168909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168909 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 28, 19, 28, 9, 19, 19, 9, 5, 9, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 19, 19, 19, 9, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/375 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488168909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168909 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 21, 12, 21, 7, 12, 12, 7, 5, 7, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 12, 12, 12, 7, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488168909 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909 Building ZINC000488168909 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488168909 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 374) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488168909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168909 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 28, 19, 28, 9, 19, 19, 9, 5, 9, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 19, 19, 19, 9, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 375) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488168909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168909 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 21, 12, 21, 7, 12, 12, 7, 5, 7, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 12, 12, 12, 7, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488168909 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168909 Building ZINC000488168912 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488168912 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/376 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488168912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168912 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 23, 22, 13, 22, 7, 13, 13, 7, 5, 7, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 13, 13, 13, 7, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/377 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488168912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168912 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 27, 18, 27, 9, 18, 18, 9, 5, 9, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 18, 18, 18, 9, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488168912 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912 Building ZINC000488168912 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488168912 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 376) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488168912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168912 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 23, 22, 13, 22, 7, 13, 13, 7, 5, 7, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 13, 13, 13, 7, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 377) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488168912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488168912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488168912 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 27, 18, 27, 9, 18, 18, 9, 5, 9, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 18, 18, 18, 9, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488168912 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488168912 Building ZINC000608245713 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608245713 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/378 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)n(C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1) `ZINC000608245713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608245713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000608245713 none Cc1nc(C)n(C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', '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.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 24, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 24, 24, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/379 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)n(C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1) `ZINC000608245713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608245713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000608245713 none Cc1nc(C)n(C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', '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.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 27, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 36, 36, 36, 36, 36, 36, 36, 27, 27, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000608245713 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713 Building ZINC000608245713 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608245713 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 378) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nc(C)n(C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1) `ZINC000608245713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608245713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000608245713 none Cc1nc(C)n(C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', '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.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 24, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 24, 24, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 379) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nc(C)n(C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1) `ZINC000608245713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608245713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000608245713 none Cc1nc(C)n(C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', '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.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 27, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 36, 36, 36, 36, 36, 36, 36, 27, 27, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000608245713 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245713 Building ZINC000608245714 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608245714 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/380 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)n(C[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1) `ZINC000608245714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608245714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000608245714 none Cc1nc(C)n(C[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', '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.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 22, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 33, 33, 33, 33, 33, 33, 33, 22, 22, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/316102/xbz-8058115.52/working/building/ZINC000608245714 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/381 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)n(C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1) `ZINC000608245714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608245714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000608245714 none Cc1nc(C)n(C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', '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.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 23, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 23, 23, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 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, 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/316102/xbz-8058115.52/working/building/ZINC000608245714 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000608245714 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714 Building ZINC000608245714 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608245714 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 380) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nc(C)n(C[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1) `ZINC000608245714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608245714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000608245714 none Cc1nc(C)n(C[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', '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.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 22, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 33, 33, 33, 33, 33, 33, 33, 22, 22, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/316102/xbz-8058115.52/working/building/ZINC000608245714 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 381) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nc(C)n(C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1) `ZINC000608245714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608245714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000608245714 none Cc1nc(C)n(C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CCO2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', '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.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 23, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 23, 23, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 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, 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/316102/xbz-8058115.52/working/building/ZINC000608245714 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000608245714 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000608245714 Building ZINC000855573772 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855573772 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/382 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F)cn1) `ZINC000855573772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855573772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000855573772 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.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', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 14, 8, 8, 1, 1, 1, 1, 5, 5, 5, 13, 13, 17, 17, 17, 27, 27, 27, 27, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 5, 13, 13, 13, 13, 27, 27, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 151 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/383 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F)cn1) `ZINC000855573772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855573772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000855573772 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.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', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 14, 7, 7, 1, 1, 1, 1, 4, 4, 4, 13, 13, 17, 17, 17, 26, 26, 26, 26, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 4, 13, 13, 13, 13, 26, 26, 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]) total number of confs: 157 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000855573772 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772 Building ZINC000855573772 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855573772 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 382) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F)cn1) `ZINC000855573772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855573772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000855573772 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.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', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 14, 8, 8, 1, 1, 1, 1, 5, 5, 5, 13, 13, 17, 17, 17, 27, 27, 27, 27, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 5, 13, 13, 13, 13, 27, 27, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 151 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 383) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F)cn1) `ZINC000855573772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855573772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000855573772 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.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', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 14, 7, 7, 1, 1, 1, 1, 4, 4, 4, 13, 13, 17, 17, 17, 26, 26, 26, 26, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 4, 13, 13, 13, 13, 26, 26, 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]) total number of confs: 157 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000855573772 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855573772 Building ZINC001719814092 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719814092 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/384 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N(C)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001719814092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719814092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001719814092 none CC(C)C(=O)N(C)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 50, 28, 42, 10, 8, 10, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 28, 28, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 182 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/385 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N(C)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001719814092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719814092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001719814092 none CC(C)C(=O)N(C)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 50, 21, 40, 10, 7, 10, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 21, 21, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 182 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719814092 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092 Building ZINC001719814092 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719814092 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 384) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)C(=O)N(C)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001719814092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719814092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001719814092 none CC(C)C(=O)N(C)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 50, 28, 42, 10, 8, 10, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 28, 28, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 182 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 385) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)C(=O)N(C)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001719814092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719814092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001719814092 none CC(C)C(=O)N(C)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 50, 21, 40, 10, 7, 10, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 21, 21, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 182 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719814092 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814092 Building ZINC001719814391 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719814391 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/386 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCNC(=O)CC1) `ZINC001719814391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719814391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001719814391 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCNC(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/387 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCNC(=O)CC1) `ZINC001719814391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719814391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001719814391 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCNC(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719814391 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391 Building ZINC001719814391 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719814391 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 386) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCNC(=O)CC1) `ZINC001719814391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719814391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001719814391 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCNC(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 387) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCNC(=O)CC1) `ZINC001719814391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719814391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001719814391 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCNC(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719814391 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814391 Building ZINC000511097644 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511097644 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/388 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000511097644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511097644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000511097644 none NS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 13, 13, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/389 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000511097644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511097644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000511097644 none NS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 33, 33, 15, 15, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 33, 33, 20, 20, 15, 15, 15, 15, 15, 15, 4, 6, 6, 4, 6, 6, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511097644 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644 Building ZINC000511097644 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511097644 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 388) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: NS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000511097644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511097644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000511097644 none NS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 13, 13, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 389) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: NS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000511097644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511097644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000511097644 none NS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 33, 33, 15, 15, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 33, 33, 20, 20, 15, 15, 15, 15, 15, 15, 4, 6, 6, 4, 6, 6, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511097644 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097644 Building ZINC000511097645 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511097645 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/390 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000511097645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511097645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000511097645 none NS(=O)(=O)C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 36, 36, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 36, 36, 19, 19, 13, 13, 13, 13, 13, 13, 4, 6, 6, 4, 6, 6, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/391 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000511097645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511097645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000511097645 none NS(=O)(=O)C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 13, 13, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511097645 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645 Building ZINC000511097645 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511097645 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 390) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: NS(=O)(=O)C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000511097645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511097645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000511097645 none NS(=O)(=O)C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 36, 36, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 36, 36, 19, 19, 13, 13, 13, 13, 13, 13, 4, 6, 6, 4, 6, 6, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 391) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: NS(=O)(=O)C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000511097645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511097645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000511097645 none NS(=O)(=O)C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 13, 13, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511097645 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511097645 Building ZINC000413914896 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000413914896 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/392 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 10, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/393 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 11, 11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 11, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/394 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/394' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 10, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/395 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/395' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 11, 11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 11, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000413914896 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 Building ZINC000413914896 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000413914896 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 392) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 10, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 393) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 11, 11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 11, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 394) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 10, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 395) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 11, 11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 11, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000413914896 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 Building ZINC000413914896 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000413914896 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 392) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 10, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 393) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 11, 11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 11, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 394) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 10, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 395) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 11, 11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 11, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000413914896 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 Building ZINC000413914896 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000413914896 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 392) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 10, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 393) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 11, 11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 11, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 394) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 10, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 395) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914896.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000413914896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914896 none COC(=O)[C@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 11, 11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 11, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000413914896 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914896 Building ZINC001281367882 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281367882 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/396 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001281367882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281367882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281367882 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 37, 44, 44, 44, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 44] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/397 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001281367882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281367882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281367882 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 32, 41, 41, 41, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281367882 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882 Building ZINC001281367882 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281367882 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 396) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001281367882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281367882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281367882 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 37, 44, 44, 44, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 44] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 397) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001281367882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281367882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281367882 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1=CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 32, 41, 41, 41, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281367882 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281367882 Building ZINC000511164810 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511164810 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/398 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1C(=O)CNC1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000511164810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511164810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000511164810 none O=C(NCCCN1C(=O)CNC1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 10, 10, 20, 20, 29, 29, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/399 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1C(=O)CNC1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000511164810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511164810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000511164810 none O=C(NCCCN1C(=O)CNC1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 10, 10, 20, 20, 29, 29, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511164810 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810 Building ZINC000511164810 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511164810 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 398) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCCN1C(=O)CNC1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000511164810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511164810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000511164810 none O=C(NCCCN1C(=O)CNC1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 10, 10, 20, 20, 29, 29, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 399) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCCN1C(=O)CNC1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000511164810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511164810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000511164810 none O=C(NCCCN1C(=O)CNC1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 10, 10, 20, 20, 29, 29, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511164810 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511164810 Building ZINC000855578200 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855578200 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/400 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F) `ZINC000855578200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855578200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000855578200 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 17, 17, 29, 29, 29, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 6, 17, 17, 17, 17, 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]) total number of confs: 234 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/401 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F) `ZINC000855578200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855578200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000855578200 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 16, 16, 27, 27, 27, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 6, 16, 16, 16, 16, 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]) total number of confs: 225 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000855578200 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200 Building ZINC000855578200 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855578200 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 400) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F) `ZINC000855578200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855578200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000855578200 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 17, 17, 29, 29, 29, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 6, 17, 17, 17, 17, 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]) total number of confs: 234 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 401) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F) `ZINC000855578200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855578200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000855578200 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 16, 16, 27, 27, 27, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 6, 16, 16, 16, 16, 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]) total number of confs: 225 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000855578200 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000855578200 Building ZINC001701829813 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701829813 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/402 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701829813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701829813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001701829813 none CN(C[C@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 4, 8, 8, 8, 37, 37, 37, 37, 37, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 4, 4, 8, 37, 37, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 132 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/403 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701829813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701829813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001701829813 none CN(C[C@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 7, 9, 9, 9, 34, 34, 34, 34, 34, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 7, 7, 9, 34, 34, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701829813 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813 Building ZINC001701829813 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701829813 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 402) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701829813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701829813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001701829813 none CN(C[C@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 4, 8, 8, 8, 37, 37, 37, 37, 37, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 4, 4, 8, 37, 37, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 132 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 403) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701829813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701829813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001701829813 none CN(C[C@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 7, 9, 9, 9, 34, 34, 34, 34, 34, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 7, 7, 9, 34, 34, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701829813 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829813 Building ZINC001701829814 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701829814 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/404 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701829814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701829814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001701829814 none CN(C[C@@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 7, 9, 9, 9, 37, 37, 37, 37, 37, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 7, 7, 9, 37, 37, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/405 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701829814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701829814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001701829814 none CN(C[C@@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 5, 8, 8, 8, 39, 39, 39, 39, 39, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 5, 5, 8, 39, 39, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701829814 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814 Building ZINC001701829814 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701829814 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 404) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701829814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701829814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001701829814 none CN(C[C@@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 7, 9, 9, 9, 37, 37, 37, 37, 37, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 7, 7, 9, 37, 37, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 405) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C[C@@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701829814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701829814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001701829814 none CN(C[C@@H](O)CNC(=O)[C@@H]1C[C@H]1c1ccco1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 5, 8, 8, 8, 39, 39, 39, 39, 39, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 5, 5, 8, 39, 39, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701829814 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701829814 Building ZINC001701838049 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001701838049 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/406 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 49, 35, 47, 30, 35, 22, 9, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 30, 30, 69, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 277 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/407 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 49, 35, 47, 30, 35, 22, 9, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 30, 30, 69, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 277 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/408 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/408' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 35, 46, 25, 35, 15, 8, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 24, 25, 48, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 252 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/409 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/409' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 35, 46, 25, 35, 15, 8, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 24, 25, 48, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 252 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701838049 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 Building ZINC001701838049 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001701838049 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 406) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 49, 35, 47, 30, 35, 22, 9, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 30, 30, 69, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 277 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 407) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 49, 35, 47, 30, 35, 22, 9, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 30, 30, 69, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 277 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 408) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 35, 46, 25, 35, 15, 8, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 24, 25, 48, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 252 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 409) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 35, 46, 25, 35, 15, 8, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 24, 25, 48, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 252 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701838049 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 Building ZINC001701838049 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001701838049 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 406) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 49, 35, 47, 30, 35, 22, 9, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 30, 30, 69, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 277 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 407) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 49, 35, 47, 30, 35, 22, 9, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 30, 30, 69, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 277 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 408) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 35, 46, 25, 35, 15, 8, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 24, 25, 48, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 252 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 409) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 35, 46, 25, 35, 15, 8, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 24, 25, 48, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 252 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701838049 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 Building ZINC001701838049 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001701838049 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 406) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 49, 35, 47, 30, 35, 22, 9, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 30, 30, 69, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 277 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 407) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 49, 35, 47, 30, 35, 22, 9, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 30, 30, 69, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 277 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 408) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 35, 46, 25, 35, 15, 8, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 24, 25, 48, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 252 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 409) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838049.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001701838049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838049 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 35, 46, 25, 35, 15, 8, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 24, 25, 48, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 252 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701838049 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838049 Building ZINC001701838050 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001701838050 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/410 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 47, 31, 46, 22, 31, 14, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 22, 22, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 236 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/411 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 47, 31, 46, 22, 31, 14, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 22, 22, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 236 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/412 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/412' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 33, 46, 30, 33, 21, 8, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 30, 30, 66, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 275 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/413 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/413' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 33, 46, 30, 33, 21, 8, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 30, 30, 66, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 275 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701838050 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 Building ZINC001701838050 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001701838050 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 410) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 47, 31, 46, 22, 31, 14, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 22, 22, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 236 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 411) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 47, 31, 46, 22, 31, 14, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 22, 22, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 236 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 412) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 33, 46, 30, 33, 21, 8, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 30, 30, 66, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 275 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 413) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 33, 46, 30, 33, 21, 8, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 30, 30, 66, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 275 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701838050 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 Building ZINC001701838050 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001701838050 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 410) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 47, 31, 46, 22, 31, 14, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 22, 22, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 236 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 411) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 47, 31, 46, 22, 31, 14, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 22, 22, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 236 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 412) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 33, 46, 30, 33, 21, 8, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 30, 30, 66, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 275 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 413) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 33, 46, 30, 33, 21, 8, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 30, 30, 66, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 275 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701838050 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 Building ZINC001701838050 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001701838050 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 410) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 47, 31, 46, 22, 31, 14, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 22, 22, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 236 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 411) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 47, 31, 46, 22, 31, 14, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 22, 22, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 236 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 412) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 33, 46, 30, 33, 21, 8, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 30, 30, 66, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 275 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 413) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001701838050.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001701838050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001701838050 none CC[C@@H]1[C@@H](C(=O)N(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 49, 33, 46, 30, 33, 21, 8, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 30, 30, 66, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 275 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701838050 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701838050 Building ZINC000511368683 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368683 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/414 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/415 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/416 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/416' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/417 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/417' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/418 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/418' -> `4.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/419 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/419' -> `5.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/420 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/420' -> `6.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/421 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/421' -> `7.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368683 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 Building ZINC000511368683 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368683 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 414) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 415) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 416) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 417) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 418) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 419) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 420) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 421) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368683 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 Building ZINC000511368683 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368683 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 414) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 415) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 416) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 417) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 418) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 419) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 420) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 421) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368683 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 Building ZINC000511368683 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368683 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 414) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 415) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 416) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 417) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 418) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 419) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 420) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 421) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368683 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 Building ZINC000511368683 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368683 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 414) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 415) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 416) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 417) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 418) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 419) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 420) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 421) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368683 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 Building ZINC000511368683 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368683 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 414) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 415) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 416) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 417) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 418) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 419) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 420) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 421) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368683 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 Building ZINC000511368683 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368683 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 414) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 415) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 416) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 417) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 418) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 419) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 420) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 421) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368683 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 Building ZINC000511368683 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368683 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 414) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 415) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 416) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 417) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 418) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 419) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 420) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 421) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368683.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368683 none C[N@]1CC[N@](C)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368683 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368683 Building ZINC000511368684 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368684 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/422 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/423 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/424 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/424' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/425 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/425' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/426 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/426' -> `4.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/427 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/427' -> `5.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/428 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/428' -> `6.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/429 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/429' -> `7.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368684 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 Building ZINC000511368684 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368684 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 422) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 423) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 424) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 425) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 426) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 427) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 428) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 429) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368684 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 Building ZINC000511368684 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368684 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 422) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 423) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 424) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 425) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 426) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 427) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 428) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 429) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368684 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 Building ZINC000511368684 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368684 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 422) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 423) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 424) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 425) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 426) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 427) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 428) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 429) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368684 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 Building ZINC000511368684 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368684 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 422) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 423) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 424) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 425) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 426) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 427) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 428) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 429) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368684 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 Building ZINC000511368684 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368684 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 422) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 423) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 424) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 425) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 426) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 427) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 428) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 429) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368684 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 Building ZINC000511368684 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368684 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 422) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 423) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 424) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 425) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 426) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 427) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 428) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 429) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368684 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 Building ZINC000511368684 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC000511368684 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 422) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 423) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 424) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 425) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `4' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 4 (index: 426) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `4.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `5' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 5 (index: 427) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `5.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `6' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 6 (index: 428) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `6.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `7' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 7 (index: 429) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000511368684.mol2' -> `7.mol2' `temp.mol2' -> `ZINC000511368684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000511368684 none C[N@]1CC[N@](C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 3, 3, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511368684 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/2.* 7: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/7.* 6: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/6.* 5: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/5.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/1.* 4: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684/4.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511368684 Building ZINC000511370124 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511370124 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/430 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(S(N)(=O)=O)cc2)cn1) `ZINC000511370124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511370124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000511370124 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(S(N)(=O)=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 25, 25, 13, 13, 33, 33, 33, 25, 25, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 13, 13, 25, 25, 33, 33, 25, 25, 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]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/431 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(S(N)(=O)=O)cc2)cn1) `ZINC000511370124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511370124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000511370124 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(S(N)(=O)=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 23, 23, 18, 23, 32, 32, 32, 23, 23, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 12, 12, 23, 23, 32, 32, 23, 23, 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511370124 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124 Building ZINC000511370124 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511370124 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 430) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(S(N)(=O)=O)cc2)cn1) `ZINC000511370124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511370124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000511370124 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(S(N)(=O)=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 25, 25, 13, 13, 33, 33, 33, 25, 25, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 13, 13, 25, 25, 33, 33, 25, 25, 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]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 431) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(S(N)(=O)=O)cc2)cn1) `ZINC000511370124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511370124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000511370124 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(S(N)(=O)=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 23, 23, 18, 23, 32, 32, 32, 23, 23, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 12, 12, 23, 23, 32, 32, 23, 23, 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511370124 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511370124 Building ZINC001719814925 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719814925 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/432 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCS(C)(=O)=O) `ZINC001719814925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719814925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001719814925 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 29, 31, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 29, 29, 31, 31, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/433 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCS(C)(=O)=O) `ZINC001719814925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719814925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001719814925 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 33, 35, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 33, 33, 35, 35, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719814925 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925 Building ZINC001719814925 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001719814925 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 432) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCS(C)(=O)=O) `ZINC001719814925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001719814925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001719814925 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 29, 31, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 29, 29, 31, 31, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 433) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCS(C)(=O)=O) `ZINC001719814925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001719814925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001719814925 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 33, 35, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 33, 33, 35, 35, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001719814925 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001719814925 Building ZINC000511531915 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511531915 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/434 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(CC(N)=O)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000511531915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511531915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000511531915 none CCOC(=O)CN(CC(N)=O)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 5, 1, 8, 11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 30, 25, 7, 25, 4, 2, 4, 9, 21, 21, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 7, 7, 9, 9, 21, 21, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/435 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(CC(N)=O)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000511531915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511531915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000511531915 none CCOC(=O)CN(CC(N)=O)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 5, 1, 8, 11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 30, 25, 7, 25, 4, 2, 4, 9, 21, 21, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 7, 7, 9, 9, 21, 21, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511531915 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915 Building ZINC000511531915 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511531915 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 434) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)CN(CC(N)=O)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000511531915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511531915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000511531915 none CCOC(=O)CN(CC(N)=O)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 5, 1, 8, 11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 30, 25, 7, 25, 4, 2, 4, 9, 21, 21, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 7, 7, 9, 9, 21, 21, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 435) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)CN(CC(N)=O)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000511531915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511531915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000511531915 none CCOC(=O)CN(CC(N)=O)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 5, 1, 8, 11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 30, 25, 7, 25, 4, 2, 4, 9, 21, 21, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 7, 7, 9, 9, 21, 21, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511531915 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511531915 Building ZINC001701855343 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701855343 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/436 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701855343.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701855343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701855343 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 50, 30, 43, 21, 30, 12, 5, 12, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 21, 21, 36, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [56, 54, 55, 50, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 229 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/437 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701855343.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701855343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701855343 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 45, 50, 35, 44, 22, 35, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 22, 22, 33, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 232 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701855343 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343 Building ZINC001701855343 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701855343 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 436) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701855343.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701855343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701855343 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 50, 30, 43, 21, 30, 12, 5, 12, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 21, 21, 36, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [56, 54, 55, 50, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 229 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 437) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701855343.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701855343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701855343 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 45, 50, 35, 44, 22, 35, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 22, 22, 33, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 232 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701855343 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855343 Building ZINC001701855344 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701855344 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/438 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701855344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701855344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701855344 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 50, 28, 41, 17, 28, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 17, 17, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 224 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/439 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701855344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701855344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701855344 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 50, 21, 39, 13, 21, 8, 4, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 13, 13, 24, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [56, 54, 55, 50, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701855344 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344 Building ZINC001701855344 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001701855344 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 438) grep: /scratch/xiaobo/316102/xbz-8058115.52/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@@H]1CCO[C@@H]1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001701855344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001701855344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701855344 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 50, 28, 41, 17, 28, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 17, 17, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 224 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 439) grep: /scratch/xiaobo/316102/xbz-8058115.52/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@@H]1CCO[C@@H]1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001701855344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001701855344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001701855344 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 50, 21, 39, 13, 21, 8, 4, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 13, 13, 24, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [56, 54, 55, 50, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001701855344 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001701855344 Building ZINC001648923686 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001648923686 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/440 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CSC[C@H]2C1) `ZINC001648923686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001648923686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001648923686 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CSC[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 1, 1, 1, 2, 8, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 8, 8, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/441 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CSC[C@H]2C1) `ZINC001648923686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001648923686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001648923686 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CSC[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 3, 1, 1, 1, 2, 8, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 9, 9, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001648923686 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686 Building ZINC001648923686 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001648923686 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 440) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CSC[C@H]2C1) `ZINC001648923686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001648923686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001648923686 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CSC[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 1, 1, 1, 2, 8, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 8, 8, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 441) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CSC[C@H]2C1) `ZINC001648923686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001648923686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001648923686 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CSC[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 3, 1, 1, 1, 2, 8, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 9, 9, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001648923686 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001648923686 Building ZINC000488302125 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488302125 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/442 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488302125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302125 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 23, 12, 23, 6, 12, 12, 6, 4, 6, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 37, 37, 37, 37, 37, 12, 12, 12, 6, 4, 4, 4, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/443 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488302125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302125 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 15, 25, 6, 15, 15, 6, 3, 6, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 5, 43, 43, 43, 43, 43, 15, 15, 15, 6, 3, 3, 3, 3, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 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]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488302125 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125 Building ZINC000488302125 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488302125 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 442) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488302125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302125 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 23, 12, 23, 6, 12, 12, 6, 4, 6, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 37, 37, 37, 37, 37, 12, 12, 12, 6, 4, 4, 4, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 443) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488302125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302125 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 15, 25, 6, 15, 15, 6, 3, 6, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 5, 43, 43, 43, 43, 43, 15, 15, 15, 6, 3, 3, 3, 3, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5] 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]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488302125 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302125 Building ZINC000488302126 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488302126 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/444 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488302126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302126 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 26, 13, 26, 7, 13, 13, 7, 3, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 40, 40, 40, 40, 40, 13, 13, 13, 7, 3, 3, 3, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/445 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488302126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302126 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 26, 14, 26, 7, 14, 14, 7, 3, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 41, 41, 41, 41, 41, 14, 14, 14, 7, 3, 3, 3, 3, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488302126 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126 Building ZINC000488302126 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488302126 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 444) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488302126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302126 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 26, 13, 26, 7, 13, 13, 7, 3, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 40, 40, 40, 40, 40, 13, 13, 13, 7, 3, 3, 3, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 445) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488302126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302126 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 26, 14, 26, 7, 14, 14, 7, 3, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 41, 41, 41, 41, 41, 14, 14, 14, 7, 3, 3, 3, 3, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488302126 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302126 Building ZINC000488302127 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488302127 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/446 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488302127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302127 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 15, 26, 6, 15, 15, 6, 3, 6, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 12, 12, 12, 5, 45, 45, 45, 45, 45, 15, 15, 15, 6, 3, 3, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5] 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]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/447 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488302127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302127 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 23, 20, 11, 20, 6, 11, 11, 6, 4, 6, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 32, 32, 32, 32, 32, 11, 11, 11, 6, 4, 4, 4, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488302127 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127 Building ZINC000488302127 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488302127 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 446) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488302127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302127 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 15, 26, 6, 15, 15, 6, 3, 6, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 12, 12, 12, 5, 45, 45, 45, 45, 45, 15, 15, 15, 6, 3, 3, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5] 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]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 447) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488302127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302127 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 23, 20, 11, 20, 6, 11, 11, 6, 4, 6, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 32, 32, 32, 32, 32, 11, 11, 11, 6, 4, 4, 4, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488302127 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302127 Building ZINC000488302128 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488302128 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/448 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488302128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302128 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 27, 14, 27, 7, 14, 14, 7, 3, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 43, 43, 43, 43, 43, 14, 14, 14, 7, 3, 3, 3, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/449 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488302128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302128 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 13, 25, 7, 13, 13, 7, 3, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 38, 38, 38, 38, 38, 13, 13, 13, 7, 3, 3, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488302128 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128 Building ZINC000488302128 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488302128 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 448) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488302128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302128 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 27, 14, 27, 7, 14, 14, 7, 3, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 43, 43, 43, 43, 43, 14, 14, 14, 7, 3, 3, 3, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 449) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000488302128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488302128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488302128 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 13, 25, 7, 13, 13, 7, 3, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 38, 38, 38, 38, 38, 13, 13, 13, 7, 3, 3, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488302128 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488302128 Building ZINC000488300332 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488300332 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/450 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488300332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300332 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 31, 31, 25, 31, 21, 25, 25, 21, 10, 21, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 47, 47, 47, 47, 47, 25, 25, 25, 21, 10, 10, 10, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/451 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488300332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300332 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 46, 40, 46, 29, 40, 40, 29, 14, 29, 6, 14, 14, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 49, 49, 49, 49, 49, 40, 40, 40, 29, 14, 14, 14, 6, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488300332 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332 Building ZINC000488300332 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488300332 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 450) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488300332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300332 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 31, 31, 25, 31, 21, 25, 25, 21, 10, 21, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 47, 47, 47, 47, 47, 25, 25, 25, 21, 10, 10, 10, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 451) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488300332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300332 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 46, 40, 46, 29, 40, 40, 29, 14, 29, 6, 14, 14, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 49, 49, 49, 49, 49, 40, 40, 40, 29, 14, 14, 14, 6, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488300332 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300332 Building ZINC000488300333 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488300333 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/452 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488300333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300333 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 30, 30, 28, 30, 15, 28, 28, 15, 9, 15, 4, 9, 9, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 48, 48, 48, 48, 48, 28, 28, 28, 15, 9, 9, 9, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/453 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488300333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300333 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 43, 43, 38, 43, 21, 38, 38, 21, 13, 21, 6, 13, 13, 6, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 48, 48, 48, 48, 48, 38, 38, 38, 21, 13, 13, 13, 6, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488300333 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333 Building ZINC000488300333 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488300333 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 452) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488300333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300333 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 30, 30, 28, 30, 15, 28, 28, 15, 9, 15, 4, 9, 9, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 48, 48, 48, 48, 48, 28, 28, 28, 15, 9, 9, 9, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 453) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488300333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300333 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 43, 43, 38, 43, 21, 38, 38, 21, 13, 21, 6, 13, 13, 6, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 48, 48, 48, 48, 48, 38, 38, 38, 21, 13, 13, 13, 6, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488300333 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300333 Building ZINC000488300334 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488300334 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/454 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488300334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300334 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 46, 38, 46, 27, 38, 38, 27, 13, 27, 6, 13, 13, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 49, 49, 49, 49, 49, 38, 38, 38, 27, 13, 13, 13, 6, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/455 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488300334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300334 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 31, 31, 26, 31, 21, 26, 26, 21, 10, 21, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 47, 47, 47, 47, 47, 26, 26, 26, 21, 10, 10, 10, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488300334 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334 Building ZINC000488300334 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488300334 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 454) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488300334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300334 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 46, 38, 46, 27, 38, 38, 27, 13, 27, 6, 13, 13, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 49, 49, 49, 49, 49, 38, 38, 38, 27, 13, 13, 13, 6, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 455) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488300334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300334 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 31, 31, 26, 31, 21, 26, 26, 21, 10, 21, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 47, 47, 47, 47, 47, 26, 26, 26, 21, 10, 10, 10, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488300334 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300334 Building ZINC000488300335 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488300335 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/456 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488300335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300335 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 43, 43, 38, 43, 21, 38, 38, 21, 13, 21, 6, 13, 13, 6, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 48, 48, 48, 48, 48, 38, 38, 38, 21, 13, 13, 13, 6, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/457 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488300335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300335 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 30, 30, 28, 30, 15, 28, 28, 15, 9, 15, 4, 9, 9, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 48, 48, 48, 48, 48, 28, 28, 28, 15, 9, 9, 9, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488300335 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335 Building ZINC000488300335 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488300335 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 456) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488300335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300335 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 43, 43, 38, 43, 21, 38, 38, 21, 13, 21, 6, 13, 13, 6, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 48, 48, 48, 48, 48, 38, 38, 38, 21, 13, 13, 13, 6, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 457) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000488300335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488300335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000488300335 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 30, 30, 28, 30, 15, 28, 28, 15, 9, 15, 4, 9, 9, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 48, 48, 48, 48, 48, 28, 28, 28, 15, 9, 9, 9, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488300335 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488300335 Building ZINC000488320479 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488320479 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/458 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488320479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320479 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 39, 46, 28, 39, 39, 28, 12, 28, 4, 12, 12, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 39, 39, 39, 28, 12, 12, 12, 4, 2, 2, 2, 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]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/459 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488320479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320479 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 45, 45, 37, 45, 22, 37, 37, 22, 10, 22, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 37, 37, 37, 22, 10, 10, 10, 4, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488320479 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479 Building ZINC000488320479 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488320479 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 458) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488320479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320479 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 39, 46, 28, 39, 39, 28, 12, 28, 4, 12, 12, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 39, 39, 39, 28, 12, 12, 12, 4, 2, 2, 2, 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]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 459) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488320479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320479 none CCOC(=O)[C@@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 45, 45, 37, 45, 22, 37, 37, 22, 10, 22, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 37, 37, 37, 22, 10, 10, 10, 4, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488320479 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320479 Building ZINC000488320485 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488320485 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/460 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488320485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320485 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 39, 45, 22, 39, 39, 22, 10, 22, 4, 10, 10, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 48, 48, 48, 48, 48, 39, 39, 39, 22, 10, 10, 10, 4, 2, 2, 2, 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]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/461 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488320485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320485 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 40, 49, 26, 40, 40, 26, 10, 26, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 40, 40, 40, 26, 10, 10, 10, 4, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488320485 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485 Building ZINC000488320485 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488320485 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 460) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488320485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320485 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 39, 45, 22, 39, 39, 22, 10, 22, 4, 10, 10, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 48, 48, 48, 48, 48, 39, 39, 39, 22, 10, 10, 10, 4, 2, 2, 2, 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]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 461) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488320485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320485 none CCOC(=O)[C@H](C)NC(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 40, 49, 26, 40, 40, 26, 10, 26, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 40, 40, 40, 26, 10, 10, 10, 4, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488320485 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320485 Building ZINC000488320486 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488320486 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/462 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488320486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320486 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 45, 45, 38, 45, 23, 38, 38, 23, 10, 23, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 38, 38, 38, 23, 10, 10, 10, 4, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/463 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488320486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320486 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 39, 46, 27, 39, 39, 27, 12, 27, 4, 12, 12, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 39, 39, 39, 27, 12, 12, 12, 4, 2, 2, 2, 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488320486 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486 Building ZINC000488320486 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488320486 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 462) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488320486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320486 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 45, 45, 38, 45, 23, 38, 38, 23, 10, 23, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 38, 38, 38, 23, 10, 10, 10, 4, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 463) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488320486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320486 none CCOC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 39, 46, 27, 39, 39, 27, 12, 27, 4, 12, 12, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 39, 39, 39, 27, 12, 12, 12, 4, 2, 2, 2, 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488320486 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320486 Building ZINC000488320489 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488320489 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/464 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488320489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320489 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 41, 49, 27, 41, 41, 27, 11, 27, 4, 11, 11, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 41, 41, 41, 27, 11, 11, 11, 4, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/465 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488320489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320489 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 44, 38, 44, 21, 38, 38, 21, 10, 21, 4, 10, 10, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 48, 48, 48, 48, 48, 38, 38, 38, 21, 10, 10, 10, 4, 2, 2, 2, 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]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488320489 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489 Building ZINC000488320489 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488320489 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 464) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488320489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320489 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 41, 49, 27, 41, 41, 27, 11, 27, 4, 11, 11, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 41, 41, 41, 27, 11, 11, 11, 4, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 465) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000488320489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488320489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000488320489 none CCOC(=O)[C@@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 44, 38, 44, 21, 38, 38, 21, 10, 21, 4, 10, 10, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 48, 48, 48, 48, 48, 38, 38, 38, 21, 10, 10, 10, 4, 2, 2, 2, 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]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488320489 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488320489 Building ZINC001343268590 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268590 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/466 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)no1) `ZINC001343268590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001343268590 none CC(C)(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 11, 25, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/467 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)no1) `ZINC001343268590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001343268590 none CC(C)(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 10, 24, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 142 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343268590 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590 Building ZINC001343268590 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268590 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 466) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)no1) `ZINC001343268590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001343268590 none CC(C)(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 11, 25, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 467) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)no1) `ZINC001343268590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001343268590 none CC(C)(C)c1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 10, 24, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 142 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343268590 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268590 Building ZINC001343268620 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268620 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/468 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1ccccc1) `ZINC001343268620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343268620 none CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 27, 49, 10, 27, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 49, 50, 50, 49, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50, 50, 49, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/469 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1ccccc1) `ZINC001343268620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343268620 none CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 22, 48, 11, 22, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 48, 50, 50, 48, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 229 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343268620 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620 Building ZINC001343268620 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268620 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 468) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1ccccc1) `ZINC001343268620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343268620 none CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 27, 49, 10, 27, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 49, 50, 50, 49, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50, 50, 49, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 469) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1ccccc1) `ZINC001343268620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343268620 none CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 22, 48, 11, 22, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 48, 50, 50, 48, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 229 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343268620 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268620 Building ZINC001343268675 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268675 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/470 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2ccccc2)C[C@@H]1O) `ZINC001343268675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343268675 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2ccccc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 7, 18, 31, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 18, 18, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 204 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/471 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2ccccc2)C[C@@H]1O) `ZINC001343268675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343268675 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2ccccc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 12, 12, 50, 50, 50, 50, 50, 50, 50, 2, 2, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343268675 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675 Building ZINC001343268675 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268675 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 470) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2ccccc2)C[C@@H]1O) `ZINC001343268675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343268675 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2ccccc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 7, 18, 31, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 18, 18, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 204 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 471) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2ccccc2)C[C@@H]1O) `ZINC001343268675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343268675 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2ccccc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 12, 25, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 12, 12, 50, 50, 50, 50, 50, 50, 50, 2, 2, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343268675 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268675 Building ZINC001343268689 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268689 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/472 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3n[nH]cc32)C[C@@H]1O) `ZINC001343268689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343268689 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3n[nH]cc32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 33, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 163 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/473 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3n[nH]cc32)C[C@@H]1O) `ZINC001343268689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343268689 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3n[nH]cc32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 30, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343268689 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689 Building ZINC001343268689 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268689 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 472) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3n[nH]cc32)C[C@@H]1O) `ZINC001343268689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343268689 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3n[nH]cc32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 33, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 163 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 473) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3n[nH]cc32)C[C@@H]1O) `ZINC001343268689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343268689 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCc3n[nH]cc32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 30, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343268689 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268689 Building ZINC001343268692 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268692 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/474 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3n[nH]cc32)C[C@@H]1O) `ZINC001343268692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343268692 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3n[nH]cc32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 29, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/475 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3n[nH]cc32)C[C@@H]1O) `ZINC001343268692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343268692 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3n[nH]cc32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 30, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343268692 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692 Building ZINC001343268692 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268692 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 474) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3n[nH]cc32)C[C@@H]1O) `ZINC001343268692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343268692 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3n[nH]cc32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 29, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 475) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3n[nH]cc32)C[C@@H]1O) `ZINC001343268692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343268692 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCc3n[nH]cc32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 30, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343268692 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343268692 Building ZINC001343269212 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269212 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/476 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1onc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343269212 none Cc1onc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 12, 8, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 23, 11, 23, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 45, 45, 45, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/477 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1onc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343269212 none Cc1onc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 12, 8, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 44, 50, 50, 23, 9, 23, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 44, 44, 44, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269212 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212 Building ZINC001343269212 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269212 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 476) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1onc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343269212 none Cc1onc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 12, 8, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 23, 11, 23, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 45, 45, 45, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 477) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1onc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343269212 none Cc1onc(C2CC2)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 12, 8, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 44, 50, 50, 23, 9, 23, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 44, 44, 44, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269212 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269212 Building ZINC001343269108 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269108 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/478 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1) `ZINC001343269108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343269108 none COc1ccc(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 45, 50, 50, 45, 10, 6, 10, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 45, 45, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/479 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1) `ZINC001343269108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343269108 none COc1ccc(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 42, 50, 50, 42, 12, 7, 12, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 42, 42, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269108 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108 Building ZINC001343269108 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269108 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 478) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccc(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1) `ZINC001343269108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343269108 none COc1ccc(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 45, 50, 50, 45, 10, 6, 10, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 45, 45, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 479) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccc(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1) `ZINC001343269108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343269108 none COc1ccc(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 42, 50, 50, 42, 12, 7, 12, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 42, 42, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269108 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269108 Building ZINC001343269148 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269148 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/480 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)o1) `ZINC001343269148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001343269148 none CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 35, 35, 35, 35, 18, 9, 18, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 50, 50, 50, 50, 50, 35, 35, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/481 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)o1) `ZINC001343269148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001343269148 none CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 36, 36, 36, 18, 9, 18, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 36, 50, 50, 50, 50, 50, 36, 36, 36, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269148 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148 Building ZINC001343269148 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269148 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 480) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)o1) `ZINC001343269148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001343269148 none CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 35, 35, 35, 35, 18, 9, 18, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 50, 50, 50, 50, 50, 35, 35, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 481) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)o1) `ZINC001343269148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001343269148 none CCc1nc(C)c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 36, 36, 36, 18, 9, 18, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 36, 50, 50, 50, 50, 50, 36, 36, 36, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269148 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269148 Building ZINC001343269491 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269491 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/482 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccncc2Cl)C[C@@H]1O) `ZINC001343269491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001343269491 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccncc2Cl)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 16, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 36, 36, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/483 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccncc2Cl)C[C@@H]1O) `ZINC001343269491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001343269491 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccncc2Cl)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 16, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 33, 33, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269491 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491 Building ZINC001343269491 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269491 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 482) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccncc2Cl)C[C@@H]1O) `ZINC001343269491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001343269491 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccncc2Cl)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 16, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 36, 36, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 483) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccncc2Cl)C[C@@H]1O) `ZINC001343269491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001343269491 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccncc2Cl)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 16, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 33, 33, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269491 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269491 Building ZINC001343269634 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269634 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/484 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cc1ncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)[nH]1) `ZINC001343269634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343269634 none CC(C)Cc1ncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 30, 30, 30, 16, 9, 16, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/485 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cc1ncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)[nH]1) `ZINC001343269634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343269634 none CC(C)Cc1ncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 28, 28, 28, 28, 18, 9, 18, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269634 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634 Building ZINC001343269634 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269634 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 484) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)Cc1ncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)[nH]1) `ZINC001343269634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343269634 none CC(C)Cc1ncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 30, 30, 30, 30, 16, 9, 16, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 485) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)Cc1ncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)[nH]1) `ZINC001343269634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343269634 none CC(C)Cc1ncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 28, 28, 28, 28, 18, 9, 18, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269634 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269634 Building ZINC001343269712 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269712 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/486 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1) `ZINC001343269712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343269712 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 26, 41, 13, 26, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 44, 50, 50, 50, 50, 50, 41, 41, 41, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/487 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1) `ZINC001343269712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343269712 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 23, 39, 12, 23, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 42, 50, 50, 50, 50, 50, 39, 39, 39, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 227 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269712 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712 Building ZINC001343269712 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269712 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 486) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1) `ZINC001343269712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343269712 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 26, 41, 13, 26, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 44, 50, 50, 50, 50, 50, 41, 41, 41, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 487) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1) `ZINC001343269712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343269712 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 23, 39, 12, 23, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 42, 50, 50, 50, 50, 50, 39, 39, 39, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 227 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269712 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269712 Building ZINC001343269716 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269716 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/488 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1) `ZINC001343269716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343269716 none C[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 24, 39, 11, 24, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 43, 50, 50, 50, 50, 50, 39, 39, 39, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/489 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1) `ZINC001343269716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343269716 none C[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 21, 38, 11, 21, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 41, 50, 50, 50, 50, 50, 38, 38, 38, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 219 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269716 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716 Building ZINC001343269716 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269716 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 488) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1) `ZINC001343269716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343269716 none C[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 24, 39, 11, 24, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 43, 50, 50, 50, 50, 50, 39, 39, 39, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 489) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1) `ZINC001343269716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343269716 none C[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 21, 38, 11, 21, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 41, 50, 50, 50, 50, 50, 38, 38, 38, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 219 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269716 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269716 Building ZINC001343269719 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269719 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/490 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn([C@H](C)CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343269719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343269719 none Cc1ccn([C@H](C)CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 31, 46, 46, 9, 8, 9, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 46, 46, 46, 31, 31, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/491 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn([C@H](C)CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343269719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343269719 none Cc1ccn([C@H](C)CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 37, 46, 46, 11, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 46, 46, 46, 37, 37, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 224 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269719 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719 Building ZINC001343269719 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269719 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 490) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccn([C@H](C)CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343269719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343269719 none Cc1ccn([C@H](C)CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 31, 46, 46, 9, 8, 9, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 46, 46, 46, 31, 31, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 491) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccn([C@H](C)CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343269719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343269719 none Cc1ccn([C@H](C)CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 37, 46, 46, 11, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 46, 46, 46, 37, 37, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 224 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269719 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269719 Building ZINC001343269722 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269722 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/492 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343269722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343269722 none Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 40, 27, 40, 40, 7, 5, 7, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 40, 40, 40, 27, 27, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/493 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343269722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343269722 none Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 41, 34, 41, 41, 11, 8, 11, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 41, 41, 41, 34, 34, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 203 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269722 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722 Building ZINC001343269722 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269722 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 492) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343269722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343269722 none Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 40, 27, 40, 40, 7, 5, 7, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 40, 40, 40, 27, 27, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 493) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343269722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343269722 none Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 41, 34, 41, 41, 11, 8, 11, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 41, 41, 41, 34, 34, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 203 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343269722 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343269722 Building ZINC001343270208 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270208 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/494 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@@H]1O) `ZINC001343270208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270208 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 14, 14, 37, 37, 37, 37, 38, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 37, 37, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/495 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@@H]1O) `ZINC001343270208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270208 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 20, 20, 39, 39, 39, 39, 41, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 39, 39, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270208 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208 Building ZINC001343270208 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270208 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 494) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@@H]1O) `ZINC001343270208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270208 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 14, 14, 37, 37, 37, 37, 38, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 37, 37, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 495) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@@H]1O) `ZINC001343270208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343270208 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnn2C2CCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 20, 20, 39, 39, 39, 39, 41, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 39, 39, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270208 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270208 Building ZINC001343270260 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270260 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/496 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)sc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343270260 none COc1cc(C)sc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 10, 23, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/497 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)sc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343270260 none COc1cc(C)sc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 142 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270260 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260 Building ZINC001343270260 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270260 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 496) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cc(C)sc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343270260 none COc1cc(C)sc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 10, 23, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 497) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cc(C)sc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343270260 none COc1cc(C)sc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 142 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270260 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270260 Building ZINC001343270433 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270433 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/498 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1oc(C2CC2)nc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343270433 none Cc1oc(C2CC2)nc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 12, 1, 5, 5, 5, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 41, 50, 50, 41, 20, 10, 20, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 41, 41, 41, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/499 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1oc(C2CC2)nc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343270433 none Cc1oc(C2CC2)nc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 12, 1, 5, 5, 5, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 42, 50, 50, 42, 21, 9, 21, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 42, 42, 42, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270433 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433 Building ZINC001343270433 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270433 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 498) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1oc(C2CC2)nc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343270433 none Cc1oc(C2CC2)nc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 12, 1, 5, 5, 5, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 41, 50, 50, 41, 20, 10, 20, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 41, 41, 41, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 499) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1oc(C2CC2)nc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343270433 none Cc1oc(C2CC2)nc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 12, 1, 5, 5, 5, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 42, 50, 50, 42, 21, 9, 21, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 42, 42, 42, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270433 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270433 Building ZINC001343270437 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270437 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/500 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 15, 37, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 37, 37] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/501 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 15, 37, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 37, 37] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/502 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/502' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 11, 34, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 34, 34] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/503 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/503' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 11, 34, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 34, 34] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270437 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 Building ZINC001343270437 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270437 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 500) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 15, 37, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 37, 37] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 501) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 15, 37, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 37, 37] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 502) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 11, 34, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 34, 34] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 503) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 11, 34, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 34, 34] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270437 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 Building ZINC001343270437 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270437 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 500) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 15, 37, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 37, 37] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 501) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 15, 37, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 37, 37] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 502) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 11, 34, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 34, 34] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 503) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 11, 34, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 34, 34] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270437 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 Building ZINC001343270437 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270437 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 500) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 15, 37, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 37, 37] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 501) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 15, 37, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 37, 37] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 502) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 11, 34, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 34, 34] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 503) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270437.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270437 none CCCN1CCC[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 11, 34, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 34, 34] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 216 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270437 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270437 Building ZINC001343270438 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270438 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/504 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 15, 35, 9, 15, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 35, 35] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/505 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 15, 35, 9, 15, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 35, 35] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/506 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/506' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 11, 33, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 33, 33] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 220 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/507 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/507' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 11, 33, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 33, 33] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 220 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270438 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 Building ZINC001343270438 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270438 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 504) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 15, 35, 9, 15, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 35, 35] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 505) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 15, 35, 9, 15, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 35, 35] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 506) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 11, 33, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 33, 33] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 220 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 507) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 11, 33, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 33, 33] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 220 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270438 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 Building ZINC001343270438 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270438 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 504) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 15, 35, 9, 15, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 35, 35] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 505) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 15, 35, 9, 15, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 35, 35] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 506) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 11, 33, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 33, 33] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 220 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 507) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 11, 33, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 33, 33] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 220 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270438 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 Building ZINC001343270438 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270438 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 504) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 15, 35, 9, 15, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 35, 35] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 505) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 35, 35, 15, 35, 9, 15, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 35, 35] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 506) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 11, 33, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 33, 33] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 220 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 507) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270438.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001343270438 none CCCN1CCC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 33, 33, 11, 33, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 33, 33] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58]) total number of confs: 220 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270438 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270438 Building ZINC001343270744 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270744 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/508 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343270744 none CCCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 18, 10, 18, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 34, 34, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/509 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343270744 none CCCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 36, 36, 36, 36, 36, 18, 9, 18, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 36, 36, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 196 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270744 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744 Building ZINC001343270744 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270744 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 508) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343270744 none CCCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 18, 10, 18, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 34, 34, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 509) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343270744 none CCCn1nccc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 36, 36, 36, 36, 36, 18, 9, 18, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 36, 36, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 196 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270744 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270744 Building ZINC001343270751 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270751 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/510 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sc1C) `ZINC001343270751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343270751 none Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 14, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 29, 12, 29, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/511 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sc1C) `ZINC001343270751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343270751 none Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 14, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270751 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751 Building ZINC001343270751 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270751 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 510) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sc1C) `ZINC001343270751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343270751 none Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 14, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 29, 12, 29, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 511) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sc1C) `ZINC001343270751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343270751 none Cc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 14, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270751 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270751 Building ZINC001343270813 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270813 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/512 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 40, 40, 40, 40, 15, 40, 11, 15, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/513 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 40, 40, 40, 40, 15, 40, 11, 15, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/514 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/514' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 11, 39, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 193 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/515 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/515' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 11, 39, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 193 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270813 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 Building ZINC001343270813 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270813 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 512) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 40, 40, 40, 40, 15, 40, 11, 15, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 513) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 40, 40, 40, 40, 15, 40, 11, 15, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 514) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 11, 39, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 193 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 515) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 11, 39, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 193 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270813 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 Building ZINC001343270813 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270813 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 512) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 40, 40, 40, 40, 15, 40, 11, 15, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 513) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 40, 40, 40, 40, 15, 40, 11, 15, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 514) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 11, 39, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 193 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 515) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 11, 39, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 193 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270813 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 Building ZINC001343270813 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270813 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 512) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 40, 40, 40, 40, 15, 40, 11, 15, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 513) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 40, 40, 40, 40, 15, 40, 11, 15, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 514) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 11, 39, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 193 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 515) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270813.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270813 none CCCN1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 11, 39, 9, 11, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 193 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270813 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270813 Building ZINC001343270815 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270815 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/516 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 41, 41, 41, 41, 15, 41, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/517 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 41, 41, 41, 41, 15, 41, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/518 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/518' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 10, 39, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/519 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/519' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 10, 39, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270815 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 Building ZINC001343270815 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270815 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 516) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 41, 41, 41, 41, 15, 41, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 517) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 41, 41, 41, 41, 15, 41, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 518) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 10, 39, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 519) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 10, 39, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270815 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 Building ZINC001343270815 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270815 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 516) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 41, 41, 41, 41, 15, 41, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 517) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 41, 41, 41, 41, 15, 41, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 518) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 10, 39, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 519) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 10, 39, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270815 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 Building ZINC001343270815 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270815 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 516) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 41, 41, 41, 41, 15, 41, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 517) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 41, 41, 41, 41, 15, 41, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 518) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 10, 39, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 519) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270815.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270815 none CCCN1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 10, 39, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270815 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270815 Building ZINC001343270844 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270844 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/520 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 36, 49, 13, 36, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 194 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/521 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 36, 49, 13, 36, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 194 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/522 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/522' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 50, 14, 41, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 189 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/523 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/523' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 50, 14, 41, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 189 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270844 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 Building ZINC001343270844 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270844 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 520) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 36, 49, 13, 36, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 194 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 521) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 36, 49, 13, 36, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 194 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 522) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 50, 14, 41, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 189 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 523) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 50, 14, 41, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 189 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270844 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 Building ZINC001343270844 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270844 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 520) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 36, 49, 13, 36, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 194 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 521) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 36, 49, 13, 36, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 194 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 522) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 50, 14, 41, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 189 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 523) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 50, 14, 41, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 189 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270844 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 Building ZINC001343270844 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270844 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 520) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 36, 49, 13, 36, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 194 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 521) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 36, 49, 13, 36, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 194 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 522) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 50, 14, 41, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 189 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 523) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270844.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270844 none CC(C)N1CCC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 50, 14, 41, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 189 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270844 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270844 Building ZINC001343270846 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270846 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/524 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 48, 35, 48, 14, 35, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 199 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/525 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 48, 35, 48, 14, 35, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 199 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/526 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/526' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 47, 47, 47, 47, 34, 47, 15, 34, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 204 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/527 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/527' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 47, 47, 47, 47, 34, 47, 15, 34, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 204 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270846 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 Building ZINC001343270846 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270846 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 524) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 48, 35, 48, 14, 35, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 199 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 525) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 48, 35, 48, 14, 35, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 199 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 526) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 47, 47, 47, 47, 34, 47, 15, 34, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 204 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 527) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 47, 47, 47, 47, 34, 47, 15, 34, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 204 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270846 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 Building ZINC001343270846 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270846 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 524) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 48, 35, 48, 14, 35, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 199 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 525) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 48, 35, 48, 14, 35, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 199 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 526) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 47, 47, 47, 47, 34, 47, 15, 34, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 204 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 527) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 47, 47, 47, 47, 34, 47, 15, 34, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 204 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270846 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 Building ZINC001343270846 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270846 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 524) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 48, 35, 48, 14, 35, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 199 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 525) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 48, 35, 48, 14, 35, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 199 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 526) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 47, 47, 47, 47, 34, 47, 15, 34, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 204 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 527) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270846.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001343270846 none CC(C)N1CCC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 47, 47, 47, 47, 34, 47, 15, 34, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55]) total number of confs: 204 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343270846 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343270846 Building ZINC001343271477 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271477 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/528 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nocc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343271477 none CC(C)c1nocc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/529 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nocc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343271477 none CC(C)c1nocc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 13, 28, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343271477 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477 Building ZINC001343271477 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271477 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 528) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)c1nocc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343271477 none CC(C)c1nocc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 529) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)c1nocc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343271477 none CC(C)c1nocc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 13, 28, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343271477 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271477 Building ZINC001343271580 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271580 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/530 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ocnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001343271580 none CC(C)(C)c1ocnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 30, 11, 30, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 151 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/531 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ocnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001343271580 none CC(C)(C)c1ocnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 36, 12, 36, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 156 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343271580 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580 Building ZINC001343271580 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271580 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 530) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)c1ocnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001343271580 none CC(C)(C)c1ocnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 30, 11, 30, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 151 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 531) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)c1ocnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001343271580 none CC(C)(C)c1ocnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 36, 12, 36, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 156 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343271580 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271580 Building ZINC001343271614 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271614 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/532 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(Cl)c1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343271614 none Cc1noc(Cl)c1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 16, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 10, 9, 10, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 28, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/533 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(Cl)c1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343271614 none Cc1noc(Cl)c1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 16, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 28, 28, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343271614 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614 Building ZINC001343271614 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271614 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 532) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1noc(Cl)c1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343271614 none Cc1noc(Cl)c1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 16, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 10, 9, 10, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 28, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 533) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1noc(Cl)c1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343271614 none Cc1noc(Cl)c1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 16, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 28, 28, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343271614 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271614 Building ZINC001343271688 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271688 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/534 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cs1) `ZINC001343271688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343271688 none COCc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 28, 28, 17, 8, 17, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 28, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 28] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 207 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/535 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cs1) `ZINC001343271688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343271688 none COCc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 27, 27, 27, 15, 8, 15, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 27, 27, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 27] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343271688 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688 Building ZINC001343271688 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271688 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 534) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cs1) `ZINC001343271688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343271688 none COCc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 28, 28, 17, 8, 17, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 28, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 28] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 207 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 535) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cs1) `ZINC001343271688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001343271688 none COCc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 27, 27, 27, 15, 8, 15, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 27, 27, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 27] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343271688 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271688 Building ZINC001343271891 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271891 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/536 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343271891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343271891 none C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 31, 37, 9, 8, 9, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 37, 50, 50, 50, 50, 50, 37, 37, 37, 31, 31, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/537 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343271891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343271891 none C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 32, 38, 10, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 38, 50, 50, 50, 50, 50, 38, 38, 38, 32, 32, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343271891 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891 Building ZINC001343271891 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271891 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 536) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343271891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343271891 none C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 31, 37, 9, 8, 9, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 37, 50, 50, 50, 50, 50, 37, 37, 37, 31, 31, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 537) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343271891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343271891 none C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 32, 38, 10, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 38, 50, 50, 50, 50, 50, 38, 38, 38, 32, 32, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343271891 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271891 Building ZINC001343271892 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271892 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/538 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343271892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343271892 none C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 26, 37, 8, 6, 8, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 37, 50, 50, 50, 50, 50, 37, 37, 37, 26, 26, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/539 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343271892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343271892 none C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 31, 39, 10, 9, 10, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 39, 50, 50, 50, 50, 50, 39, 39, 39, 31, 31, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 207 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343271892 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892 Building ZINC001343271892 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271892 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 538) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343271892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343271892 none C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 26, 37, 8, 6, 8, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 37, 50, 50, 50, 50, 50, 37, 37, 37, 26, 26, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 539) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343271892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343271892 none C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 31, 39, 10, 9, 10, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 39, 50, 50, 50, 50, 50, 39, 39, 39, 31, 31, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 207 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343271892 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343271892 Building ZINC000413914889 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000413914889 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/540 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 10, 10, 10, 10, 10, 10, 10, 6, 1, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 10, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/541 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 11, 29, 11, 11, 11, 11, 11, 11, 11, 5, 1, 7, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 11, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/542 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/542' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 10, 10, 10, 10, 10, 10, 10, 6, 1, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 10, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/543 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/543' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 11, 29, 11, 11, 11, 11, 11, 11, 11, 5, 1, 7, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 11, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000413914889 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 Building ZINC000413914889 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000413914889 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 540) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 10, 10, 10, 10, 10, 10, 10, 6, 1, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 10, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 541) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 11, 29, 11, 11, 11, 11, 11, 11, 11, 5, 1, 7, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 11, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 542) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 10, 10, 10, 10, 10, 10, 10, 6, 1, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 10, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 543) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 11, 29, 11, 11, 11, 11, 11, 11, 11, 5, 1, 7, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 11, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000413914889 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 Building ZINC000413914889 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000413914889 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 540) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 10, 10, 10, 10, 10, 10, 10, 6, 1, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 10, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 541) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 11, 29, 11, 11, 11, 11, 11, 11, 11, 5, 1, 7, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 11, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 542) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 10, 10, 10, 10, 10, 10, 10, 6, 1, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 10, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 543) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 11, 29, 11, 11, 11, 11, 11, 11, 11, 5, 1, 7, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 11, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000413914889 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 Building ZINC000413914889 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000413914889 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 540) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 10, 10, 10, 10, 10, 10, 10, 6, 1, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 10, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 541) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 11, 29, 11, 11, 11, 11, 11, 11, 11, 5, 1, 7, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 11, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 542) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 10, 10, 10, 10, 10, 10, 10, 6, 1, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 10, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 543) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000413914889.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000413914889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000413914889 none COC(=O)[C@@H]1CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 11, 29, 11, 11, 11, 11, 11, 11, 11, 5, 1, 7, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 11, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/316102/xbz-8058115.52/working/building/ZINC000413914889 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000413914889 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000413914889 Building ZINC000746210688 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000746210688 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/544 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000746210688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000746210688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000746210688 none CNS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 31, 31, 27, 31, 31, 21, 21, 21, 21, 10, 2, 13, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50, 50, 31, 27, 31, 31, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/545 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000746210688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000746210688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000746210688 none CNS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 31, 31, 26, 31, 31, 21, 21, 21, 21, 10, 1, 13, 1, 1, 1, 2, 2, 2, 21, 21, 50, 50, 50, 50, 31, 26, 31, 31, 21, 21, 21, 21, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21] 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000746210688 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688 Building ZINC000746210688 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000746210688 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 544) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000746210688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000746210688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000746210688 none CNS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 31, 31, 27, 31, 31, 21, 21, 21, 21, 10, 2, 13, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50, 50, 31, 27, 31, 31, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 545) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000746210688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000746210688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000746210688 none CNS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 31, 31, 26, 31, 31, 21, 21, 21, 21, 10, 1, 13, 1, 1, 1, 2, 2, 2, 21, 21, 50, 50, 50, 50, 31, 26, 31, 31, 21, 21, 21, 21, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21] 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000746210688 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000746210688 Building ZINC000511951032 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511951032 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/546 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1C(=O)CNC1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000511951032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511951032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000511951032 none O=C(NCCN1C(=O)CNC1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 18, 31, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 18, 18, 31, 31, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/547 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1C(=O)CNC1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000511951032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511951032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000511951032 none O=C(NCCN1C(=O)CNC1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 18, 31, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 2, 3, 3, 3, 18, 18, 31, 31, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511951032 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032 Building ZINC000511951032 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511951032 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 546) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCN1C(=O)CNC1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000511951032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511951032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000511951032 none O=C(NCCN1C(=O)CNC1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 18, 31, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 18, 18, 31, 31, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 547) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCN1C(=O)CNC1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000511951032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511951032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000511951032 none O=C(NCCN1C(=O)CNC1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 18, 31, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 2, 3, 3, 3, 18, 18, 31, 31, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000511951032 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000511951032 Building ZINC000488863422 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488863422 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/548 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488863422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488863422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000488863422 none CNS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 12 rigid atoms, others: [32, 33, 2, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 34, 14, 13, 16, 15, 29, 30, 31] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 21 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/549 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488863422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488863422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000488863422 none CNS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 21, 21, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 11, 11, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488863422 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422 Building ZINC000488863422 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488863422 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 548) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488863422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488863422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000488863422 none CNS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 12 rigid atoms, others: [32, 33, 2, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 34, 14, 13, 16, 15, 29, 30, 31] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 21 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 549) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488863422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488863422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000488863422 none CNS(=O)(=O)C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 21, 21, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 11, 11, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488863422 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863422 Building ZINC000488863424 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488863424 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/550 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488863424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488863424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000488863424 none CNS(=O)(=O)C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 12, 17, 17, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 19, 19, 19, 19, 12, 12, 7, 7, 7, 7, 7, 7, 6, 8, 8, 8, 8, 8, 8, 8, 8] 34 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/551 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488863424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488863424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000488863424 none CNS(=O)(=O)C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 2, 8, 8, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 15 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 30 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488863424 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424 Building ZINC000488863424 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488863424 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 550) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNS(=O)(=O)C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488863424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488863424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000488863424 none CNS(=O)(=O)C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 12, 17, 17, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 19, 19, 19, 19, 12, 12, 7, 7, 7, 7, 7, 7, 6, 8, 8, 8, 8, 8, 8, 8, 8] 34 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 551) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNS(=O)(=O)C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488863424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488863424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000488863424 none CNS(=O)(=O)C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 2, 8, 8, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 15 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 30 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000488863424 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000488863424 Building ZINC001281534839 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281534839 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/552 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)[C@H]2CC[C@@H](C(N)=O)O2)CC1) `ZINC001281534839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281534839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281534839 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)[C@H]2CC[C@@H](C(N)=O)O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 14, 21, 24, 35, 35, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 24, 24, 35, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/553 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)[C@H]2CC[C@@H](C(N)=O)O2)CC1) `ZINC001281534839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281534839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281534839 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)[C@H]2CC[C@@H](C(N)=O)O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 19, 23, 29, 29, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 23, 23, 29, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281534839 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839 Building ZINC001281534839 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281534839 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 552) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)[C@H]2CC[C@@H](C(N)=O)O2)CC1) `ZINC001281534839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281534839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281534839 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)[C@H]2CC[C@@H](C(N)=O)O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 14, 21, 24, 35, 35, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 24, 24, 35, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 553) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)[C@H]2CC[C@@H](C(N)=O)O2)CC1) `ZINC001281534839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281534839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281534839 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCC1(CNC(=O)[C@H]2CC[C@@H](C(N)=O)O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 19, 23, 29, 29, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 23, 23, 29, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281534839 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281534839 Building ZINC000512482321 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000512482321 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/554 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 11, 11, 16, 16, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/555 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/556 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/556' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 11, 11, 16, 16, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/557 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/557' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000512482321 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 Building ZINC000512482321 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000512482321 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 554) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 11, 11, 16, 16, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 555) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 556) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 11, 11, 16, 16, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 557) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000512482321 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 Building ZINC000512482321 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000512482321 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 554) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 11, 11, 16, 16, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 555) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 556) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 11, 11, 16, 16, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 557) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000512482321 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 Building ZINC000512482321 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000512482321 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 554) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 11, 11, 16, 16, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 555) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 556) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 25, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 11, 11, 16, 16, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 557) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000512482321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000512482321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000512482321 none O=C(NCCN1CCNC(=O)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 2, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000512482321 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512482321 Building ZINC000512628816 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000512628816 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/558 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NCC(N)=O)cc2)cn1) `ZINC000512628816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512628816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000512628816 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NCC(N)=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 8, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 13, 13, 13, 24, 32, 32, 4, 4, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 4, 4, 13, 24, 24, 32, 32, 4, 4, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/559 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NCC(N)=O)cc2)cn1) `ZINC000512628816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512628816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000512628816 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NCC(N)=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 8, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 13, 13, 13, 25, 30, 30, 4, 4, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 4, 4, 13, 25, 25, 30, 30, 4, 4, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000512628816 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816 Building ZINC000512628816 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000512628816 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 558) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NCC(N)=O)cc2)cn1) `ZINC000512628816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512628816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000512628816 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NCC(N)=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 8, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 13, 13, 13, 24, 32, 32, 4, 4, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 4, 4, 13, 24, 24, 32, 32, 4, 4, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 559) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NCC(N)=O)cc2)cn1) `ZINC000512628816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512628816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000512628816 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NCC(N)=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 8, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 13, 13, 13, 25, 30, 30, 4, 4, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 4, 4, 13, 25, 25, 30, 30, 4, 4, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000512628816 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512628816 Building ZINC000512640362 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000512640362 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/560 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCC(N)=O)cc1) `ZINC000512640362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512640362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000512640362 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCC(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', '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.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 5, 17, 17, 17, 43, 49, 49, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 17, 43, 43, 49, 49, 6, 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/561 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCC(N)=O)cc1) `ZINC000512640362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512640362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000512640362 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCC(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', '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.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 16, 16, 16, 41, 49, 49, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 16, 41, 41, 49, 49, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000512640362 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362 Building ZINC000512640362 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000512640362 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 560) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCC(N)=O)cc1) `ZINC000512640362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512640362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000512640362 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCC(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', '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.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 5, 17, 17, 17, 43, 49, 49, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 17, 43, 43, 49, 49, 6, 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 561) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCC(N)=O)cc1) `ZINC000512640362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512640362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000512640362 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCC(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', '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.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 16, 16, 16, 41, 49, 49, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 16, 41, 41, 49, 49, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000512640362 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000512640362 Building ZINC000489041915 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489041915 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/562 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000489041915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489041915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000489041915 none COCCC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 19, 19, 13, 19, 13, 13, 13, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 13, 13, 28, 28, 28, 19, 19, 19, 19, 13, 13, 13, 13, 13, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 13, 13, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/563 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000489041915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489041915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000489041915 none COCCC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 16, 16, 11, 16, 11, 11, 11, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 11, 11, 28, 28, 28, 16, 16, 16, 16, 11, 11, 11, 11, 11, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 11, 11, 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, 53]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000489041915 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915 Building ZINC000489041915 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489041915 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 562) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000489041915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489041915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000489041915 none COCCC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 19, 19, 13, 19, 13, 13, 13, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 13, 13, 28, 28, 28, 19, 19, 19, 19, 13, 13, 13, 13, 13, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 13, 13, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 563) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000489041915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489041915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000489041915 none COCCC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 16, 16, 11, 16, 11, 11, 11, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 11, 11, 28, 28, 28, 16, 16, 16, 16, 11, 11, 11, 11, 11, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 11, 11, 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, 53]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000489041915 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000489041915 Building ZINC001343454486 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343454486 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/564 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCN2CCCC2)[C@@H](O)C1) `ZINC001343454486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343454486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001343454486 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCN2CCCC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 9, 9, 9, 25, 18, 42, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 25, 25, 26, 26, 35, 36, 50, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 221 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/565 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCN2CCCC2)[C@@H](O)C1) `ZINC001343454486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343454486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001343454486 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCN2CCCC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 25, 19, 44, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 25, 25, 28, 28, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 6, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 7, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 219 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343454486 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486 Building ZINC001343454486 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343454486 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 564) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCN2CCCC2)[C@@H](O)C1) `ZINC001343454486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343454486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001343454486 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCN2CCCC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 9, 9, 9, 25, 18, 42, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 25, 25, 26, 26, 35, 36, 50, 50, 50, 50, 50, 50, 50, 50, 12, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 221 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 565) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCN2CCCC2)[C@@H](O)C1) `ZINC001343454486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343454486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001343454486 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCN2CCCC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 25, 19, 44, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 25, 25, 28, 28, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 6, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 7, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 219 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343454486 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343454486 Building ZINC001281605990 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281605990 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/566 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281605990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281605990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001281605990 none CN(C)C(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 50, 27, 22, 7, 6, 7, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 42, 42, 32, 32, 22, 22, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 240 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/567 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281605990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281605990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001281605990 none CN(C)C(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 27, 24, 8, 6, 8, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 41, 41, 31, 31, 24, 24, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 228 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281605990 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990 Building ZINC001281605990 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281605990 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 566) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)C(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281605990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281605990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001281605990 none CN(C)C(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 50, 27, 22, 7, 6, 7, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 42, 42, 32, 32, 22, 22, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 240 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 567) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)C(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281605990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281605990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001281605990 none CN(C)C(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 27, 24, 8, 6, 8, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 41, 41, 31, 31, 24, 24, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 228 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281605990 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281605990 Building ZINC001281606951 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281606951 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/568 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281606951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281606951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001281606951 none CNC(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 21, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 37, 37, 25, 25, 16, 16, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/569 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281606951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281606951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001281606951 none CNC(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 25, 23, 9, 6, 9, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 41, 41, 31, 31, 23, 23, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281606951 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951 Building ZINC001281606951 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281606951 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 568) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281606951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281606951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001281606951 none CNC(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 21, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 37, 37, 25, 25, 16, 16, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 569) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281606951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281606951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001281606951 none CNC(=O)CCCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 25, 23, 9, 6, 9, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 41, 41, 31, 31, 23, 23, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281606951 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281606951 Building ZINC001281607365 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281607365 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/570 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCC(N)=O)C[C@H]21) `ZINC001281607365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281607365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281607365 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCC(N)=O)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 18, 20, 33, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 14, 20, 20, 20, 20, 33, 33, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/571 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCC(N)=O)C[C@H]21) `ZINC001281607365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281607365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281607365 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCC(N)=O)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 14, 18, 21, 34, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 14, 14, 21, 21, 21, 21, 34, 34, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281607365 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365 Building ZINC001281607365 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281607365 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 570) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCC(N)=O)C[C@H]21) `ZINC001281607365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281607365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281607365 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCC(N)=O)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 18, 20, 33, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 14, 20, 20, 20, 20, 33, 33, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 571) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCC(N)=O)C[C@H]21) `ZINC001281607365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281607365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281607365 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCC(N)=O)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 14, 18, 21, 34, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 14, 14, 21, 21, 21, 21, 34, 34, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281607365 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607365 Building ZINC001281607403 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281607403 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/572 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCNC(N)=O)C[C@H]21) `ZINC001281607403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281607403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281607403 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCNC(N)=O)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 13, 17, 19, 36, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 13, 13, 19, 19, 19, 19, 36, 36, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/573 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCNC(N)=O)C[C@H]21) `ZINC001281607403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281607403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281607403 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCNC(N)=O)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 14, 19, 20, 35, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 14, 14, 20, 20, 20, 20, 35, 35, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281607403 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403 Building ZINC001281607403 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281607403 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 572) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCNC(N)=O)C[C@H]21) `ZINC001281607403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281607403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281607403 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCNC(N)=O)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 13, 17, 19, 36, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 13, 13, 19, 19, 19, 19, 36, 36, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 573) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCNC(N)=O)C[C@H]21) `ZINC001281607403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281607403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281607403 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)CCCCNC(N)=O)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 14, 19, 20, 35, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 14, 14, 20, 20, 20, 20, 35, 35, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281607403 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607403 Building ZINC001281607420 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281607420 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/574 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281607420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281607420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281607420 none CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 28, 14, 28, 28, 7, 14, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 36, 28, 28, 28, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/575 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281607420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281607420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281607420 none CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 27, 12, 27, 27, 6, 12, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 37, 27, 27, 27, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 214 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281607420 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420 Building ZINC001281607420 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281607420 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 574) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281607420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281607420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281607420 none CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 28, 14, 28, 28, 7, 14, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 36, 28, 28, 28, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 575) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281607420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281607420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281607420 none CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 27, 12, 27, 27, 6, 12, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 37, 27, 27, 27, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 214 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281607420 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607420 Building ZINC001281607421 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281607421 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/576 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281607421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281607421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281607421 none CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 29, 12, 29, 29, 6, 12, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 33, 29, 29, 29, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/577 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281607421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281607421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281607421 none CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 25, 13, 25, 25, 8, 13, 8, 8, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 32, 25, 25, 25, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281607421 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421 Building ZINC001281607421 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281607421 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 576) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281607421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281607421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281607421 none CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 29, 12, 29, 29, 6, 12, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 33, 29, 29, 29, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 577) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001281607421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281607421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281607421 none CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 25, 13, 25, 25, 8, 13, 8, 8, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 32, 25, 25, 25, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281607421 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281607421 Building ZINC000107281958 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107281958 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/578 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/578' -> `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)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 4, 11, 11, 11, 11, 32, 34, 34, 34, 34, 34, 34, 34, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/579 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/579' -> `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)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/580 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/580' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 4, 11, 11, 11, 11, 32, 34, 34, 34, 34, 34, 34, 34, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/581 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/581' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000107281958 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 Building ZINC000107281958 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107281958 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 578) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 4, 11, 11, 11, 11, 32, 34, 34, 34, 34, 34, 34, 34, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 579) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 580) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 4, 11, 11, 11, 11, 32, 34, 34, 34, 34, 34, 34, 34, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 581) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000107281958 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 Building ZINC000107281958 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107281958 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 578) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 4, 11, 11, 11, 11, 32, 34, 34, 34, 34, 34, 34, 34, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 579) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 580) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 4, 11, 11, 11, 11, 32, 34, 34, 34, 34, 34, 34, 34, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 581) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000107281958 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 Building ZINC000107281958 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107281958 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 578) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 4, 11, 11, 11, 11, 32, 34, 34, 34, 34, 34, 34, 34, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 579) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 580) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 4, 11, 11, 11, 11, 32, 34, 34, 34, 34, 34, 34, 34, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 581) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1) `ZINC000107281958.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107281958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281958 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000107281958 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281958 Building ZINC000107281961 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107281961 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/582 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/582' -> `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)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 5, 12, 12, 12, 12, 34, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 84 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/583 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/583' -> `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)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 14, 14, 14, 14, 39, 40, 40, 40, 40, 40, 40, 40, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 22, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 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, 52, 53, 54, 55, 56]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/584 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/584' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 5, 12, 12, 12, 12, 34, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 84 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/585 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/585' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 14, 14, 14, 14, 39, 40, 40, 40, 40, 40, 40, 40, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 22, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 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, 52, 53, 54, 55, 56]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000107281961 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 Building ZINC000107281961 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107281961 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 582) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 5, 12, 12, 12, 12, 34, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 84 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 583) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 14, 14, 14, 14, 39, 40, 40, 40, 40, 40, 40, 40, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 22, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 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, 52, 53, 54, 55, 56]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 584) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 5, 12, 12, 12, 12, 34, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 84 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 585) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 14, 14, 14, 14, 39, 40, 40, 40, 40, 40, 40, 40, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 22, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 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, 52, 53, 54, 55, 56]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000107281961 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 Building ZINC000107281961 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107281961 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 582) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 5, 12, 12, 12, 12, 34, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 84 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 583) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 14, 14, 14, 14, 39, 40, 40, 40, 40, 40, 40, 40, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 22, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 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, 52, 53, 54, 55, 56]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 584) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 5, 12, 12, 12, 12, 34, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 84 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 585) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 14, 14, 14, 14, 39, 40, 40, 40, 40, 40, 40, 40, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 22, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 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, 52, 53, 54, 55, 56]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000107281961 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 Building ZINC000107281961 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107281961 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 582) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 5, 12, 12, 12, 12, 34, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 84 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 583) grep: /scratch/xiaobo/316102/xbz-8058115.52/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 14, 14, 14, 14, 39, 40, 40, 40, 40, 40, 40, 40, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 22, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 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, 52, 53, 54, 55, 56]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 584) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 5, 12, 12, 12, 12, 34, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 84 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 585) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCN(C[C@H]2CCCCN2C)CC1) `ZINC000107281961.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107281961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107281961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCCN2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 14, 14, 14, 14, 39, 40, 40, 40, 40, 40, 40, 40, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 22, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 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, 52, 53, 54, 55, 56]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000107281961 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000107281961 Building ZINC001281609760 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281609760 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/586 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001281609760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281609760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001281609760 none CNC(=O)CCCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 23, 21, 5, 4, 5, 4, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 41, 42, 28, 28, 21, 21, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/587 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001281609760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281609760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001281609760 none CNC(=O)CCCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 21, 23, 9, 6, 9, 6, 6, 6, 6, 6, 6, 3, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 39, 36, 28, 28, 23, 23, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281609760 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760 Building ZINC001281609760 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281609760 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 586) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)CCCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001281609760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281609760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001281609760 none CNC(=O)CCCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 23, 21, 5, 4, 5, 4, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 41, 42, 28, 28, 21, 21, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 587) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)CCCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001281609760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281609760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001281609760 none CNC(=O)CCCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 21, 23, 9, 6, 9, 6, 6, 6, 6, 6, 6, 3, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 39, 36, 28, 28, 23, 23, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281609760 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281609760 Building ZINC001343479485 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343479485 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/588 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)COCC2CCCC2)[C@@H](O)C1) `ZINC001343479485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343479485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343479485 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)COCC2CCCC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 16, 40, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 53, 54] set([13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/589 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)COCC2CCCC2)[C@@H](O)C1) `ZINC001343479485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343479485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343479485 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)COCC2CCCC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 22, 34, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 16, 16, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 53, 54] set([13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343479485 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485 Building ZINC001343479485 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343479485 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 588) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)COCC2CCCC2)[C@@H](O)C1) `ZINC001343479485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343479485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343479485 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)COCC2CCCC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 16, 40, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 53, 54] set([13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 589) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)COCC2CCCC2)[C@@H](O)C1) `ZINC001343479485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343479485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343479485 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)COCC2CCCC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 22, 34, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 16, 16, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 53, 54] set([13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343479485 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343479485 Building ZINC000173420632 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000173420632 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/590 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 22, 22, 22, 22, 22, 14, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/591 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 15, 26, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 26, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/592 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/592' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 22, 22, 22, 22, 22, 14, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/593 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/593' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 15, 26, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 26, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000173420632 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 Building ZINC000173420632 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000173420632 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 590) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 22, 22, 22, 22, 22, 14, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 591) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 15, 26, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 26, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 592) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 22, 22, 22, 22, 22, 14, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 593) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 15, 26, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 26, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000173420632 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 Building ZINC000173420632 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000173420632 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 590) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 22, 22, 22, 22, 22, 14, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 591) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 15, 26, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 26, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 592) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 22, 22, 22, 22, 22, 14, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 593) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 15, 26, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 26, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000173420632 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 Building ZINC000173420632 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000173420632 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 590) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 22, 22, 22, 22, 22, 14, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 591) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 15, 26, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 26, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 592) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 22, 22, 22, 22, 22, 14, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 593) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420632.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000173420632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420632 none CNc1cc(N2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 15, 26, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 26, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000173420632 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420632 Building ZINC000173420618 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000173420618 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/594 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 15, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/595 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 23, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/596 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/596' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 15, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/597 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/597' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 23, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000173420618 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 Building ZINC000173420618 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000173420618 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 594) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 15, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 595) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 23, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 596) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 15, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 597) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 23, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000173420618 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 Building ZINC000173420618 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000173420618 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 594) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 15, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 595) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 23, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 596) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 15, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 597) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 23, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000173420618 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 Building ZINC000173420618 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000173420618 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 594) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 15, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 595) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 23, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 596) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 15, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 597) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1) `ZINC000173420618.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000173420618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000173420618 none CNc1cc(N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 23, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000173420618 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000173420618 Building ZINC000667067897 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000667067897 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/598 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC000667067897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000667067897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000667067897 none CN(CCc1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/599 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC000667067897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000667067897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000667067897 none CN(CCc1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 1, 1, 1, 3, 3, 3, 10, 10, 10, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 3, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000667067897 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897 Building ZINC000667067897 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000667067897 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 598) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(CCc1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC000667067897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000667067897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000667067897 none CN(CCc1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 599) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(CCc1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC000667067897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000667067897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000667067897 none CN(CCc1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 1, 1, 1, 3, 3, 3, 10, 10, 10, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 3, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000667067897 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000667067897 Building ZINC000416105285 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416105285 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/600 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000416105285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416105285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416105285 none COC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 32, 10, 10, 3, 10, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 24, 24, 10, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/601 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000416105285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416105285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416105285 none COC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 27, 10, 10, 4, 10, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 24, 24, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/316102/xbz-8058115.52/working/building/ZINC000416105285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416105285 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285 Building ZINC000416105285 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416105285 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 600) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000416105285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416105285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416105285 none COC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 32, 10, 10, 3, 10, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 24, 24, 10, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 601) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000416105285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416105285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416105285 none COC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 27, 10, 10, 4, 10, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 24, 24, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/316102/xbz-8058115.52/working/building/ZINC000416105285 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416105285 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105285 Building ZINC000416105288 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416105288 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/602 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000416105288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416105288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416105288 none COC(=O)CNC(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 30, 10, 10, 3, 10, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 26, 26, 10, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/603 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000416105288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416105288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416105288 none COC(=O)CNC(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 29, 10, 10, 3, 10, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 24, 24, 10, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416105288 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288 Building ZINC000416105288 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416105288 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 602) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CNC(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000416105288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416105288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416105288 none COC(=O)CNC(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 30, 10, 10, 3, 10, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 26, 26, 10, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 603) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CNC(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000416105288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416105288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416105288 none COC(=O)CNC(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 29, 10, 10, 3, 10, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 24, 24, 10, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416105288 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416105288 Building ZINC001343490590 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343490590 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/604 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343490590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343490590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001343490590 none CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 42, 26, 21, 11, 21, 21, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 21, 21, 21, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 230 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/605 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343490590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343490590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001343490590 none CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 41, 25, 21, 12, 21, 21, 12, 12, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 21, 21, 21, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 230 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343490590 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590 Building ZINC001343490590 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343490590 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 604) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343490590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343490590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001343490590 none CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 42, 26, 21, 11, 21, 21, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 21, 21, 21, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 230 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 605) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343490590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343490590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001343490590 none CC(C)CCO[C@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 41, 25, 21, 12, 21, 21, 12, 12, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 21, 21, 21, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 230 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343490590 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490590 Building ZINC001343490591 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343490591 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/606 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343490591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343490591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001343490591 none CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 29, 26, 13, 26, 26, 13, 13, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 26, 26, 26, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/607 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343490591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343490591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001343490591 none CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 43, 30, 22, 11, 22, 22, 11, 11, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 22, 22, 22, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 227 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343490591 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591 Building ZINC001343490591 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343490591 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 606) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343490591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343490591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001343490591 none CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 29, 26, 13, 26, 26, 13, 13, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 26, 26, 26, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 607) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343490591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343490591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001343490591 none CC(C)CCO[C@@H](C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 43, 30, 22, 11, 22, 22, 11, 11, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 22, 22, 22, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 227 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343490591 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343490591 Building ZINC001281632386 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281632386 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/608 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCCC(N)=O)[C@@H]2C1) `ZINC001281632386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281632386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281632386 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCCC(N)=O)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 10, 10, 28, 32, 34, 45, 50, 50, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 28, 28, 34, 34, 34, 34, 45, 45, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/609 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCCC(N)=O)[C@@H]2C1) `ZINC001281632386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281632386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281632386 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCCC(N)=O)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 8, 8, 8, 9, 9, 26, 30, 33, 42, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 26, 26, 33, 33, 33, 33, 42, 42, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281632386 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386 Building ZINC001281632386 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281632386 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 608) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCCC(N)=O)[C@@H]2C1) `ZINC001281632386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281632386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281632386 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCCC(N)=O)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 10, 10, 28, 32, 34, 45, 50, 50, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 28, 28, 34, 34, 34, 34, 45, 45, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 609) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCCC(N)=O)[C@@H]2C1) `ZINC001281632386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281632386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281632386 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCCC(N)=O)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 8, 8, 8, 9, 9, 26, 30, 33, 42, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 26, 26, 33, 33, 33, 33, 42, 42, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281632386 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632386 Building ZINC001281632652 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281632652 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/610 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCn3cncn3)[C@@H]2C1) `ZINC001281632652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281632652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281632652 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCn3cncn3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 5, 8, 8, 29, 22, 42, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 29, 29, 32, 32, 40, 37, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/611 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCn3cncn3)[C@@H]2C1) `ZINC001281632652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281632652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281632652 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCn3cncn3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 8, 8, 30, 22, 47, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 30, 30, 33, 33, 43, 39, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281632652 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652 Building ZINC001281632652 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281632652 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 610) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCn3cncn3)[C@@H]2C1) `ZINC001281632652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281632652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281632652 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCn3cncn3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 5, 8, 8, 29, 22, 42, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 29, 29, 32, 32, 40, 37, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 611) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCn3cncn3)[C@@H]2C1) `ZINC001281632652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281632652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281632652 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)CCCn3cncn3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 8, 8, 30, 22, 47, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 30, 30, 33, 33, 43, 39, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281632652 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281632652 Building ZINC001343506935 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343506935 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/612 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 48, 50, 28, 11, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/613 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 48, 50, 28, 11, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/614 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/614' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 23, 10, 10, 10, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/615 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/615' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 23, 10, 10, 10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343506935 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 Building ZINC001343506935 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343506935 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 612) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 48, 50, 28, 11, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 613) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 48, 50, 28, 11, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 614) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 23, 10, 10, 10, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 615) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 23, 10, 10, 10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343506935 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 Building ZINC001343506935 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343506935 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 612) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 48, 50, 28, 11, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 613) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 48, 50, 28, 11, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 614) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 23, 10, 10, 10, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 615) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 23, 10, 10, 10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343506935 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 Building ZINC001343506935 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343506935 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 612) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 48, 50, 28, 11, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 613) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 48, 50, 28, 11, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 614) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 23, 10, 10, 10, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 615) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1) `ZINC001343506935.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343506935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001343506935 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 23, 10, 10, 10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343506935 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343506935 Building ZINC001281649886 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281649886 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/616 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001281649886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281649886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281649886 none CCCc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 26, 8, 6, 8, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 26, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/617 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001281649886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281649886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281649886 none CCCc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 22, 22, 22, 22, 22, 8, 5, 8, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 22, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281649886 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886 Building ZINC001281649886 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281649886 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 616) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001281649886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281649886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281649886 none CCCc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 26, 26, 8, 6, 8, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 26, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 617) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001281649886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281649886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281649886 none CCCc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 22, 22, 22, 22, 22, 8, 5, 8, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 22, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281649886 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649886 Building ZINC001281649821 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281649821 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/618 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1) `ZINC001281649821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281649821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281649821 none CO[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 21, 43, 10, 21, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 44, 50, 50, 50, 50, 43, 43, 43, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/619 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1) `ZINC001281649821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281649821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281649821 none CO[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 41, 17, 41, 8, 17, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 42, 50, 50, 50, 50, 42, 42, 42, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 222 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281649821 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821 Building ZINC001281649821 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281649821 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 618) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1) `ZINC001281649821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281649821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281649821 none CO[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 21, 43, 10, 21, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 44, 50, 50, 50, 50, 43, 43, 43, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 619) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1) `ZINC001281649821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281649821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281649821 none CO[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 41, 17, 41, 8, 17, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 42, 50, 50, 50, 50, 42, 42, 42, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 222 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281649821 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649821 Building ZINC001281649823 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281649823 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/620 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1) `ZINC001281649823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281649823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281649823 none CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 40, 22, 40, 10, 22, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 43, 50, 50, 50, 50, 41, 41, 41, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 212 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/621 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1) `ZINC001281649823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281649823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281649823 none CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 45, 25, 45, 10, 25, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 45, 50, 50, 50, 50, 46, 46, 46, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281649823 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823 Building ZINC001281649823 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281649823 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 620) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1) `ZINC001281649823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281649823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281649823 none CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 40, 22, 40, 10, 22, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 43, 50, 50, 50, 50, 41, 41, 41, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 212 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 621) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1) `ZINC001281649823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281649823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281649823 none CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 45, 25, 45, 10, 25, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 45, 50, 50, 50, 50, 46, 46, 46, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281649823 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649823 Building ZINC001281651147 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281651147 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/622 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001281651147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001281651147 none CC(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 50, 44, 44, 20, 7, 20, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 44, 44, 50, 50, 50, 50, 50, 50, 50, 44, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 44] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/623 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001281651147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001281651147 none CC(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 50, 45, 45, 21, 10, 21, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 45, 45, 50, 50, 50, 50, 50, 50, 50, 45, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 45] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651147 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147 Building ZINC001281651147 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281651147 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 622) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001281651147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001281651147 none CC(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 50, 44, 44, 20, 7, 20, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 44, 44, 50, 50, 50, 50, 50, 50, 50, 44, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 44] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 623) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001281651147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001281651147 none CC(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 50, 45, 45, 21, 10, 21, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 45, 45, 50, 50, 50, 50, 50, 50, 50, 45, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 45] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651147 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651147 Building ZINC001281651198 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281651198 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/624 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001281651198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281651198 none CC(C)(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 11, 24, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/625 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001281651198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281651198 none CC(C)(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 21, 9, 21, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651198 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198 Building ZINC001281651198 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281651198 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 624) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001281651198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281651198 none CC(C)(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 11, 24, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 625) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001281651198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281651198 none CC(C)(C)n1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 21, 9, 21, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651198 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651198 Building ZINC001281649950 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281649950 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/626 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3cnccc3[nH]2)C[C@H]1O) `ZINC001281649950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281649950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001281649950 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3cnccc3[nH]2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/627 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3cnccc3[nH]2)C[C@H]1O) `ZINC001281649950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281649950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001281649950 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3cnccc3[nH]2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281649950 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950 Building ZINC001281649950 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281649950 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 626) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3cnccc3[nH]2)C[C@H]1O) `ZINC001281649950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281649950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001281649950 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3cnccc3[nH]2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 627) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3cnccc3[nH]2)C[C@H]1O) `ZINC001281649950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281649950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001281649950 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3cnccc3[nH]2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281649950 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281649950 Building ZINC001281650143 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650143 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/628 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001281650143 none Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 44, 50, 50, 24, 10, 24, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 44, 44, 44, 44, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/629 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001281650143 none Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 24, 8, 24, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 45, 45, 45, 45, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650143 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143 Building ZINC001281650143 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650143 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 628) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001281650143 none Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 44, 50, 50, 24, 10, 24, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 44, 44, 44, 44, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 629) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001281650143 none Cn1ncc(C2CC2)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 24, 8, 24, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 45, 45, 45, 45, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650143 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650143 Building ZINC001281650163 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650163 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/630 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281650163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001281650163 none Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 38, 46, 46, 13, 7, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 46, 46, 46, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/631 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281650163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001281650163 none Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 38, 46, 46, 14, 9, 14, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 46, 46, 46, 38, 38, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650163 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163 Building ZINC001281650163 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650163 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 630) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281650163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001281650163 none Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 38, 46, 46, 13, 7, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 46, 46, 46, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 631) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281650163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001281650163 none Cc1ccn([C@@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 38, 46, 46, 14, 9, 14, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 46, 46, 46, 38, 38, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650163 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650163 Building ZINC001281650165 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650165 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/632 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn([C@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281650165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001281650165 none Cc1ccn([C@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 37, 46, 46, 15, 8, 15, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 46, 46, 46, 37, 37, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/633 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn([C@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281650165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001281650165 none Cc1ccn([C@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 36, 46, 46, 13, 8, 13, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 46, 46, 46, 36, 36, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650165 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165 Building ZINC001281650165 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650165 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 632) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccn([C@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281650165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001281650165 none Cc1ccn([C@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 37, 46, 46, 15, 8, 15, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 46, 46, 46, 37, 37, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 633) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccn([C@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281650165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001281650165 none Cc1ccn([C@H](C)CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 36, 46, 46, 13, 8, 13, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 46, 46, 46, 36, 36, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650165 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650165 Building ZINC001281650227 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650227 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/634 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001281650227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001281650227 none CCN(CC)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 33, 45, 50, 29, 33, 10, 29, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 33, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 45, 45, 45, 45, 45, 45, 45] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 313 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/635 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001281650227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001281650227 none CCN(CC)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 35, 44, 50, 29, 35, 8, 29, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 35, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 44, 44, 44, 44, 44, 44, 44] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 301 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650227 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227 Building ZINC001281650227 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650227 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 634) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCN(CC)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001281650227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001281650227 none CCN(CC)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 33, 45, 50, 29, 33, 10, 29, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 33, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 45, 45, 45, 45, 45, 45, 45] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 313 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 635) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCN(CC)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001281650227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001281650227 none CCN(CC)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 35, 44, 50, 29, 35, 8, 29, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 35, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 44, 44, 44, 44, 44, 44, 44] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 301 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650227 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650227 Building ZINC001281650228 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650228 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/636 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001281650228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001281650228 none CCN(CC)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 37, 46, 50, 32, 37, 10, 32, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 37, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 46, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 287 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/637 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001281650228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001281650228 none CCN(CC)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 35, 46, 50, 29, 35, 9, 29, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 35, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 46, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 293 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650228 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228 Building ZINC001281650228 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650228 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 636) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCN(CC)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001281650228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001281650228 none CCN(CC)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 37, 46, 50, 32, 37, 10, 32, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 37, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 46, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 287 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 637) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCN(CC)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001281650228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001281650228 none CCN(CC)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 35, 46, 50, 29, 35, 9, 29, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 35, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 46, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 293 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650228 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650228 Building ZINC001281650232 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650232 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/638 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)oc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001281650232 none Cc1cc(=O)oc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 30, 10, 30, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/639 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)oc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001281650232 none Cc1cc(=O)oc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 29, 9, 29, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650232 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232 Building ZINC001281650232 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650232 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 638) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1cc(=O)oc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001281650232 none Cc1cc(=O)oc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 30, 10, 30, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 639) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1cc(=O)oc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001281650232 none Cc1cc(=O)oc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 29, 9, 29, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650232 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650232 Building ZINC001281650293 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650293 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/640 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001281650293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001281650293 none COc1cccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 10, 6, 10, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 31, 31, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/641 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001281650293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001281650293 none COc1cccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 7, 4, 7, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 31, 31, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650293 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293 Building ZINC001281650293 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650293 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 640) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001281650293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001281650293 none COc1cccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 10, 6, 10, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 31, 31, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 641) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001281650293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001281650293 none COc1cccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 7, 4, 7, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 31, 31, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650293 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650293 Building ZINC001281650302 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650302 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/642 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCCCC2)C[C@H]1O) `ZINC001281650302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001281650302 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCCCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 15, 15, 15, 15, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 222 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/643 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCCCC2)C[C@H]1O) `ZINC001281650302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001281650302 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCCCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 218 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650302 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302 Building ZINC001281650302 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650302 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 642) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCCCC2)C[C@H]1O) `ZINC001281650302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001281650302 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCCCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 15, 15, 15, 15, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 222 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 643) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCCCC2)C[C@H]1O) `ZINC001281650302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001281650302 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCCCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 218 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650302 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650302 Building ZINC001281650571 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650571 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/644 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1) `ZINC001281650571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281650571 none CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 50, 31, 50, 50, 31, 13, 31, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/645 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1) `ZINC001281650571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281650571 none CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 50, 43, 50, 50, 34, 11, 34, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650571 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571 Building ZINC001281650571 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650571 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 644) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1) `ZINC001281650571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281650571 none CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 50, 31, 50, 50, 31, 13, 31, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 645) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1) `ZINC001281650571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281650571 none CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 50, 43, 50, 50, 34, 11, 34, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650571 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650571 Building ZINC001281650610 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650610 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/646 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)Cc1ccoc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001281650610 none CN(C)Cc1ccoc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 37, 37, 37, 37, 37, 11, 8, 11, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/647 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)Cc1ccoc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001281650610 none CN(C)Cc1ccoc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 39, 39, 39, 39, 39, 12, 9, 12, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650610 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610 Building ZINC001281650610 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650610 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 646) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)Cc1ccoc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001281650610 none CN(C)Cc1ccoc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 37, 37, 37, 37, 37, 11, 8, 11, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 647) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)Cc1ccoc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001281650610 none CN(C)Cc1ccoc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 39, 39, 39, 39, 39, 12, 9, 12, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650610 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650610 Building ZINC001281650706 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650706 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/648 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001281650706 none COCc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 32, 32, 32, 32, 15, 10, 15, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 32, 32, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/649 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001281650706 none COCc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 30, 30, 30, 30, 30, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 30, 30, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650706 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706 Building ZINC001281650706 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650706 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 648) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001281650706 none COCc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 32, 32, 32, 32, 15, 10, 15, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 32, 32, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 649) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281650706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001281650706 none COCc1ccsc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 30, 30, 30, 30, 30, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 30, 30, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650706 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650706 Building ZINC001281650819 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650819 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/650 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001281650819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001281650819 none CN(C)c1ccnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/651 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001281650819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001281650819 none CN(C)c1ccnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 15, 8, 15, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 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/316102/xbz-8058115.52/working/building/ZINC001281650819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650819 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819 Building ZINC001281650819 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650819 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 650) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)c1ccnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001281650819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001281650819 none CN(C)c1ccnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 651) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)c1ccnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001281650819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001281650819 none CN(C)c1ccnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 15, 8, 15, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 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/316102/xbz-8058115.52/working/building/ZINC001281650819 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650819 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650819 Building ZINC001281650854 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650854 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/652 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C1CC1) `ZINC001281650854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281650854 none Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 22, 9, 22, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 45, 45, 50, 50, 45, 45, 45, 45, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 149 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/653 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C1CC1) `ZINC001281650854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281650854 none Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 25, 9, 25, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 45, 45, 50, 50, 45, 45, 45, 45, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 149 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650854 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854 Building ZINC001281650854 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281650854 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 652) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C1CC1) `ZINC001281650854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281650854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281650854 none Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 22, 9, 22, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 45, 45, 50, 50, 45, 45, 45, 45, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 149 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 653) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C1CC1) `ZINC001281650854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281650854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281650854 none Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 25, 9, 25, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 45, 45, 50, 50, 45, 45, 45, 45, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 149 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281650854 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281650854 Building ZINC001281652448 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652448 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/654 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001281652448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281652448 none COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 34, 30, 11, 30, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 34, 34, 34, 50, 50, 50, 50, 50, 41, 41, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 34, 34, 34, 34, 34, 34] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 228 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/655 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001281652448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281652448 none COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 34, 30, 9, 30, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 34, 34, 34, 50, 50, 50, 50, 50, 42, 42, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34, 34, 34, 34, 34] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 222 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652448 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448 Building ZINC001281652448 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652448 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 654) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001281652448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281652448 none COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 34, 30, 11, 30, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 34, 34, 34, 50, 50, 50, 50, 50, 41, 41, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 34, 34, 34, 34, 34, 34] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 228 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 655) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001281652448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281652448 none COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 34, 30, 9, 30, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 34, 34, 34, 50, 50, 50, 50, 50, 42, 42, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34, 34, 34, 34, 34] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 222 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652448 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652448 Building ZINC001281652516 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652516 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/656 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001281652516 none CCCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 12, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 32, 32, 32, 32, 32, 14, 7, 14, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/657 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001281652516 none CCCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 12, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 31, 31, 31, 14, 6, 14, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652516 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516 Building ZINC001281652516 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652516 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 656) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001281652516 none CCCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 12, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 32, 32, 32, 32, 32, 14, 7, 14, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 657) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001281652516 none CCCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 12, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 31, 31, 31, 14, 6, 14, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652516 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652516 Building ZINC001281652555 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652555 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/658 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3ccncc3n2)C[C@H]1O) `ZINC001281652555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001281652555 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3ccncc3n2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/659 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3ccncc3n2)C[C@H]1O) `ZINC001281652555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001281652555 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3ccncc3n2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652555 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555 Building ZINC001281652555 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652555 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 658) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3ccncc3n2)C[C@H]1O) `ZINC001281652555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001281652555 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3ccncc3n2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 659) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3ccncc3n2)C[C@H]1O) `ZINC001281652555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001281652555 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3ccncc3n2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652555 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652555 Building ZINC001281652562 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652562 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/660 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001281652562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281652562 none CCc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 29, 29, 21, 6, 4, 6, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 29, 29, 50, 50, 50, 50, 50, 29, 29, 21, 21, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 29] 150 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 50, 51, 52]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/661 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001281652562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281652562 none CCc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 29, 29, 22, 8, 5, 8, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 29, 29, 50, 50, 50, 50, 50, 29, 29, 22, 22, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652562 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562 Building ZINC001281652562 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652562 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 660) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001281652562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281652562 none CCc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 29, 29, 21, 6, 4, 6, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 29, 29, 50, 50, 50, 50, 50, 29, 29, 21, 21, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 29] 150 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 50, 51, 52]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 661) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001281652562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281652562 none CCc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 29, 29, 22, 8, 5, 8, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 29, 29, 50, 50, 50, 50, 50, 29, 29, 22, 22, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652562 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652562 Building ZINC001281652824 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652824 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/662 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC23CCOCC3)C[C@H]1O) `ZINC001281652824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281652824 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC23CCOCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 22, 22, 36, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/663 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC23CCOCC3)C[C@H]1O) `ZINC001281652824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281652824 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC23CCOCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 21, 21, 35, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652824 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824 Building ZINC001281652824 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652824 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 662) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC23CCOCC3)C[C@H]1O) `ZINC001281652824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281652824 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC23CCOCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 22, 22, 36, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 663) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC23CCOCC3)C[C@H]1O) `ZINC001281652824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281652824 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC23CCOCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 21, 21, 35, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652824 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652824 Building ZINC001281652825 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652825 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/664 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CC23CCOCC3)C[C@H]1O) `ZINC001281652825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281652825 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CC23CCOCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 23, 23, 45, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/665 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CC23CCOCC3)C[C@H]1O) `ZINC001281652825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281652825 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CC23CCOCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 23, 23, 45, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652825 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825 Building ZINC001281652825 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652825 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 664) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CC23CCOCC3)C[C@H]1O) `ZINC001281652825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281652825 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CC23CCOCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 23, 23, 45, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 665) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CC23CCOCC3)C[C@H]1O) `ZINC001281652825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001281652825 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CC23CCOCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 23, 23, 45, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652825 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652825 Building ZINC001281652834 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281652834 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/666 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 50, 10, 26, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 169 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/667 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 50, 10, 26, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 169 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/668 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/668' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/669 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/669' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652834 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 Building ZINC001281652834 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281652834 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 666) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 50, 10, 26, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 169 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 667) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 50, 10, 26, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 169 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 668) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 669) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652834 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 Building ZINC001281652834 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281652834 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 666) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 50, 10, 26, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 169 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 667) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 50, 10, 26, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 169 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 668) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 669) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652834 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 Building ZINC001281652834 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281652834 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 666) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 50, 10, 26, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 169 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 667) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 50, 10, 26, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 169 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 668) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 669) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652834.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281652834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652834 none CC(C)N1CCCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 50, 9, 25, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 170 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652834 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652834 Building ZINC001281652835 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281652835 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/670 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 27, 50, 10, 27, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 173 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/671 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 27, 50, 10, 27, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 173 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/672 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/672' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 175 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/673 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/673' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 175 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652835 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 Building ZINC001281652835 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281652835 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 670) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 27, 50, 10, 27, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 173 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 671) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 27, 50, 10, 27, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 173 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 672) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 175 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 673) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 175 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652835 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 Building ZINC001281652835 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281652835 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 670) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 27, 50, 10, 27, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 173 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 671) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 27, 50, 10, 27, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 173 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 672) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 175 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 673) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 175 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652835 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 Building ZINC001281652835 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281652835 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 670) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 27, 50, 10, 27, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 173 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 671) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 27, 50, 10, 27, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 173 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 672) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 175 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 673) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652835.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281652835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281652835 none CC(C)N1CCCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [56, 54, 55, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 57, 58]) total number of confs: 175 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652835 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652835 Building ZINC001281652841 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652841 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/674 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2F)C[C@H]1O) `ZINC001281652841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001281652841 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 28, 28, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/675 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2F)C[C@H]1O) `ZINC001281652841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001281652841 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 29, 29, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652841 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841 Building ZINC001281652841 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652841 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 674) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2F)C[C@H]1O) `ZINC001281652841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001281652841 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 28, 28, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 675) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2F)C[C@H]1O) `ZINC001281652841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001281652841 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc(F)c2F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 29, 29, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652841 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652841 Building ZINC001281652868 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652868 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/676 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCN2CCCCC2)C[C@H]1O) `ZINC001281652868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281652868 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCN2CCCCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 15, 15, 28, 31, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/677 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCN2CCCCC2)C[C@H]1O) `ZINC001281652868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281652868 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCN2CCCCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 15, 15, 30, 33, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652868 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868 Building ZINC001281652868 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652868 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 676) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCN2CCCCC2)C[C@H]1O) `ZINC001281652868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281652868 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCN2CCCCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 15, 15, 28, 31, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 677) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCN2CCCCC2)C[C@H]1O) `ZINC001281652868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281652868 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCN2CCCCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 15, 15, 30, 33, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652868 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652868 Building ZINC001281651637 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281651637 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/678 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 7, 23, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 168 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/679 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 7, 23, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 168 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/680 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/680' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 183 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/681 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/681' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 183 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651637 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 Building ZINC001281651637 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281651637 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 678) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 7, 23, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 168 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 679) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 7, 23, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 168 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 680) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 183 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 681) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 183 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651637 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 Building ZINC001281651637 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281651637 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 678) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 7, 23, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 168 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 679) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 7, 23, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 168 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 680) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 183 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 681) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 183 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651637 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 Building ZINC001281651637 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281651637 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 678) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 7, 23, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 168 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 679) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 7, 23, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 168 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 680) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 183 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 681) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651637.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651637 none CC(C)CN1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 183 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651637 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651637 Building ZINC001281651638 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281651638 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/682 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 7, 18, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/683 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 7, 18, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/684 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/684' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 8, 23, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 165 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/685 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/685' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 8, 23, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 165 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651638 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 Building ZINC001281651638 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281651638 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 682) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 7, 18, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 683) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 7, 18, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 684) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 8, 23, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 165 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 685) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 8, 23, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 165 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651638 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 Building ZINC001281651638 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281651638 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 682) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 7, 18, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 683) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 7, 18, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 684) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 8, 23, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 165 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 685) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 8, 23, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 165 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651638 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 Building ZINC001281651638 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001281651638 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 682) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 7, 18, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 683) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 50, 7, 18, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 684) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 8, 23, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 165 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 685) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001281651638.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001281651638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001281651638 none CC(C)CN1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 8, 23, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58]) total number of confs: 165 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651638 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651638 Building ZINC001281651658 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281651658 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/686 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(F)(F)F)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281651658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001281651658 none C[C@H](CC(F)(F)F)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 15, 15, 15, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 29, 40, 40, 50, 50, 50, 50, 12, 29, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 40, 40, 40, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/687 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(F)(F)F)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281651658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001281651658 none C[C@H](CC(F)(F)F)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 15, 15, 15, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 29, 40, 40, 50, 50, 50, 50, 12, 29, 12, 12, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 40, 40, 40, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651658 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658 Building ZINC001281651658 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281651658 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 686) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](CC(F)(F)F)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281651658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001281651658 none C[C@H](CC(F)(F)F)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 15, 15, 15, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 29, 40, 40, 50, 50, 50, 50, 12, 29, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 40, 40, 40, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 687) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](CC(F)(F)F)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281651658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001281651658 none C[C@H](CC(F)(F)F)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 15, 15, 15, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 29, 40, 40, 50, 50, 50, 50, 12, 29, 12, 12, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 40, 40, 40, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651658 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651658 Building ZINC001281651913 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281651913 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/688 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]c3ncccc23)C[C@H]1O) `ZINC001281651913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001281651913 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]c3ncccc23)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 8, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 3, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/689 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]c3ncccc23)C[C@H]1O) `ZINC001281651913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001281651913 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]c3ncccc23)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 8, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 3, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651913 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913 Building ZINC001281651913 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281651913 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 688) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]c3ncccc23)C[C@H]1O) `ZINC001281651913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001281651913 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]c3ncccc23)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 8, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 3, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 689) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]c3ncccc23)C[C@H]1O) `ZINC001281651913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001281651913 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2c[nH]c3ncccc23)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 8, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 3, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651913 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651913 Building ZINC001281651993 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281651993 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/690 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281651993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281651993 none Cc1csc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 32, 31, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 32, 32, 31, 31, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/691 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281651993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281651993 none Cc1csc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 30, 28, 13, 10, 13, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 30, 30, 28, 28, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651993 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993 Building ZINC001281651993 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281651993 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 690) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1csc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281651993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281651993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281651993 none Cc1csc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 32, 31, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 32, 32, 31, 31, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 691) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1csc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281651993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281651993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001281651993 none Cc1csc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 30, 28, 13, 10, 13, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 30, 30, 28, 28, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281651993 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281651993 Building ZINC001281652031 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652031 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/692 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281652031 none C[C@@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 15, 33, 33, 50, 50, 50, 50, 50, 50, 9, 15, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 33, 33, 33, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/693 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281652031 none C[C@@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 19, 36, 36, 49, 50, 50, 50, 50, 50, 11, 19, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 36, 36, 36, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 192 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652031 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031 Building ZINC001281652031 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652031 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 692) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281652031 none C[C@@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 15, 33, 33, 50, 50, 50, 50, 50, 50, 9, 15, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 33, 33, 33, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 693) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281652031 none C[C@@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 19, 36, 36, 49, 50, 50, 50, 50, 50, 11, 19, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 36, 36, 36, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 192 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652031 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652031 Building ZINC001281652032 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652032 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/694 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281652032 none C[C@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 14, 34, 34, 49, 50, 50, 50, 50, 50, 7, 14, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 34, 34, 34, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/695 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281652032 none C[C@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 18, 38, 38, 50, 50, 50, 50, 50, 50, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 38, 38, 38, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652032 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032 Building ZINC001281652032 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652032 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 694) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281652032 none C[C@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 14, 34, 34, 49, 50, 50, 50, 50, 50, 7, 14, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 34, 34, 34, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 695) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001281652032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281652032 none C[C@H](Oc1ccccn1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 18, 38, 38, 50, 50, 50, 50, 50, 50, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 38, 38, 38, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652032 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652032 Building ZINC001281652156 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652156 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/696 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281652156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001281652156 none CC(C)(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 26, 11, 26, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/697 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281652156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001281652156 none CC(C)(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 10, 23, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652156 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156 Building ZINC001281652156 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281652156 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 696) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281652156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281652156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001281652156 none CC(C)(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 26, 11, 26, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 697) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001281652156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281652156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001281652156 none CC(C)(C)n1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 10, 23, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281652156 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281652156 Building ZINC001702128441 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702128441 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/698 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCOC3)C[C@H]21) `ZINC001702128441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702128441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128441 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 13, 27, 34, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 13, 13, 33, 33, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/699 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCOC3)C[C@H]21) `ZINC001702128441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702128441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128441 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 13, 27, 37, 50, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 13, 13, 36, 36, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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/316102/xbz-8058115.52/working/building/ZINC001702128441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702128441 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441 Building ZINC001702128441 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702128441 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 698) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCOC3)C[C@H]21) `ZINC001702128441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702128441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128441 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 13, 27, 34, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 13, 13, 33, 33, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 699) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCOC3)C[C@H]21) `ZINC001702128441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702128441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128441 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 13, 27, 37, 50, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 13, 13, 36, 36, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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/316102/xbz-8058115.52/working/building/ZINC001702128441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702128441 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128441 Building ZINC001702128442 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702128442 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/700 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCOC3)C[C@H]21) `ZINC001702128442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702128442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128442 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 13, 27, 33, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 13, 13, 30, 30, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/701 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCOC3)C[C@H]21) `ZINC001702128442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702128442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128442 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 15, 31, 39, 50, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 15, 15, 36, 36, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702128442 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442 Building ZINC001702128442 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702128442 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 700) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCOC3)C[C@H]21) `ZINC001702128442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702128442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128442 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 13, 27, 33, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 13, 13, 30, 30, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 701) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCOC3)C[C@H]21) `ZINC001702128442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702128442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128442 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 15, 31, 39, 50, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 15, 15, 36, 36, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702128442 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128442 Building ZINC001702128783 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702128783 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/702 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001702128783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702128783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702128783 none CCOCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 29, 15, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 43, 43, 29, 29, 7, 7, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/703 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001702128783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702128783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702128783 none CCOCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 31, 16, 5, 4, 5, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 44, 44, 16, 16, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702128783 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783 Building ZINC001702128783 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702128783 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 702) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001702128783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702128783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702128783 none CCOCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 29, 15, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 43, 43, 29, 29, 7, 7, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 703) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001702128783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702128783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702128783 none CCOCCOCC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 31, 16, 5, 4, 5, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 44, 44, 16, 16, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702128783 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128783 Building ZINC001702128991 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702128991 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/704 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCCO3)C[C@H]21) `ZINC001702128991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702128991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128991 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCCO3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 17, 36, 47, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 17, 17, 45, 45, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/705 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCCO3)C[C@H]21) `ZINC001702128991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702128991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128991 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCCO3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 8, 8, 19, 39, 48, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 19, 19, 46, 46, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702128991 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991 Building ZINC001702128991 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702128991 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 704) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCCO3)C[C@H]21) `ZINC001702128991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702128991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128991 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCCO3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 17, 36, 47, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 17, 17, 45, 45, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 705) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCCO3)C[C@H]21) `ZINC001702128991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702128991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128991 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@H]3CCCO3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 8, 8, 19, 39, 48, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 19, 19, 46, 46, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702128991 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128991 Building ZINC001702128992 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702128992 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/706 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCCO3)C[C@H]21) `ZINC001702128992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702128992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128992 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCCO3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 19, 37, 47, 50, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 19, 19, 46, 46, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/707 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCCO3)C[C@H]21) `ZINC001702128992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702128992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128992 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCCO3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 8, 8, 18, 37, 44, 50, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 18, 18, 44, 44, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702128992 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992 Building ZINC001702128992 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702128992 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 706) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCCO3)C[C@H]21) `ZINC001702128992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702128992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128992 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCCO3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 19, 37, 47, 50, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 19, 19, 46, 46, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 707) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCCO3)C[C@H]21) `ZINC001702128992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702128992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001702128992 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)COC[C@@H]3CCCO3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 8, 8, 18, 37, 44, 50, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 18, 18, 44, 44, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702128992 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702128992 Building ZINC001281665034 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281665034 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/708 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC2CCOCC2)C1) `ZINC001281665034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281665034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281665034 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 31, 41, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 7, 31, 31, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/709 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC2CCOCC2)C1) `ZINC001281665034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281665034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281665034 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 33, 36, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 9, 33, 33, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281665034 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034 Building ZINC001281665034 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281665034 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 708) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC2CCOCC2)C1) `ZINC001281665034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281665034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281665034 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 31, 41, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 7, 31, 31, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 709) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC2CCOCC2)C1) `ZINC001281665034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281665034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281665034 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCC2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 33, 36, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 9, 33, 33, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281665034 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281665034 Building ZINC001281668029 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281668029 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/710 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCN2CCCCC2)C1) `ZINC001281668029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281668029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001281668029 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCN2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 29, 25, 42, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 8, 29, 29, 35, 35, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/711 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCN2CCCCC2)C1) `ZINC001281668029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281668029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001281668029 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCN2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 28, 23, 41, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 28, 28, 33, 33, 37, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281668029 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029 Building ZINC001281668029 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281668029 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 710) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCN2CCCCC2)C1) `ZINC001281668029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281668029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001281668029 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCN2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 29, 25, 42, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 8, 29, 29, 35, 35, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 711) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCN2CCCCC2)C1) `ZINC001281668029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281668029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001281668029 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCN2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 28, 23, 41, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 28, 28, 33, 33, 37, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281668029 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281668029 Building ZINC001702140414 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702140414 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/712 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001702140414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702140414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702140414 none CCOCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 39, 28, 17, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 49, 49, 39, 39, 17, 17, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/713 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001702140414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702140414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702140414 none CCOCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 40, 29, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 49, 49, 40, 40, 16, 16, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702140414 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414 Building ZINC001702140414 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702140414 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 712) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001702140414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702140414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702140414 none CCOCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 39, 28, 17, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 49, 49, 39, 39, 17, 17, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 713) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001702140414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702140414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702140414 none CCOCCOCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 40, 29, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 49, 49, 40, 40, 16, 16, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702140414 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702140414 Building ZINC001281673302 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281673302 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/714 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2nccs2)C1) `ZINC001281673302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281673302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001281673302 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2nccs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 24, 30, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 7, 24, 24, 30, 30, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/715 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2nccs2)C1) `ZINC001281673302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281673302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001281673302 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2nccs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 30, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 7, 25, 25, 30, 30, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281673302 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302 Building ZINC001281673302 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281673302 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 714) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2nccs2)C1) `ZINC001281673302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281673302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001281673302 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2nccs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 24, 30, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 7, 24, 24, 30, 30, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 715) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2nccs2)C1) `ZINC001281673302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281673302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001281673302 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2nccs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 30, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 7, 25, 25, 30, 30, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281673302 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281673302 Building ZINC000416298435 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298435 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/716 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 177 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/717 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 177 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/718 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/718' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 12, 3, 14, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 18, 24, 27, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 24, 24, 27, 27, 81] 150 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/719 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/719' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 12, 3, 14, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 18, 24, 27, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 24, 24, 27, 27, 81] 150 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298435 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 Building ZINC000416298435 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298435 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 716) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 177 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 717) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 177 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 718) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 12, 3, 14, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 18, 24, 27, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 24, 24, 27, 27, 81] 150 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 719) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 12, 3, 14, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 18, 24, 27, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 24, 24, 27, 27, 81] 150 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298435 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 Building ZINC000416298435 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298435 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 716) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 177 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 717) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 177 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 718) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 12, 3, 14, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 18, 24, 27, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 24, 24, 27, 27, 81] 150 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 719) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 12, 3, 14, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 18, 24, 27, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 24, 24, 27, 27, 81] 150 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298435 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 Building ZINC000416298435 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298435 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 716) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 177 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 717) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 177 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 718) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 12, 3, 14, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 18, 24, 27, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 24, 24, 27, 27, 81] 150 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 719) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298435.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298435 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 12, 3, 14, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 18, 24, 27, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 24, 24, 27, 27, 81] 150 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298435 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298435 Building ZINC000416298439 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298439 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/720 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 6, 1, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 18, 22, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 18, 18, 22, 22, 66] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/721 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 6, 1, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 18, 22, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 18, 18, 22, 22, 66] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/722 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/722' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 13, 25, 28, 13, 13, 13, 13, 13, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 25, 25, 28, 28, 84] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/723 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/723' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 13, 25, 28, 13, 13, 13, 13, 13, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 25, 25, 28, 28, 84] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298439 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 Building ZINC000416298439 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298439 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 720) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 6, 1, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 18, 22, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 18, 18, 22, 22, 66] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 721) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 6, 1, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 18, 22, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 18, 18, 22, 22, 66] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 722) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 13, 25, 28, 13, 13, 13, 13, 13, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 25, 25, 28, 28, 84] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 723) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 13, 25, 28, 13, 13, 13, 13, 13, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 25, 25, 28, 28, 84] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298439 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 Building ZINC000416298439 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298439 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 720) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 6, 1, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 18, 22, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 18, 18, 22, 22, 66] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 721) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 6, 1, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 18, 22, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 18, 18, 22, 22, 66] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 722) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 13, 25, 28, 13, 13, 13, 13, 13, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 25, 25, 28, 28, 84] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 723) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 13, 25, 28, 13, 13, 13, 13, 13, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 25, 25, 28, 28, 84] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298439 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 Building ZINC000416298439 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298439 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 720) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 6, 1, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 18, 22, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 18, 18, 22, 22, 66] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 721) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 6, 1, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 18, 22, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 18, 18, 22, 22, 66] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 722) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 13, 25, 28, 13, 13, 13, 13, 13, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 25, 25, 28, 28, 84] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 723) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO) `ZINC000416298439.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298439 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 13, 25, 28, 13, 13, 13, 13, 13, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 13, 25, 25, 28, 28, 84] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298439 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298439 Building ZINC000416298441 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298441 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/724 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 7, 7, 7, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 12, 21, 25, 12, 12, 12, 12, 12, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 21, 21, 25, 25, 75] 150 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]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/725 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 7, 7, 7, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 12, 21, 25, 12, 12, 12, 12, 12, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 21, 21, 25, 25, 75] 150 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]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/726 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/726' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/727 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/727' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298441 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 Building ZINC000416298441 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298441 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 724) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 7, 7, 7, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 12, 21, 25, 12, 12, 12, 12, 12, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 21, 21, 25, 25, 75] 150 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]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 725) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 7, 7, 7, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 12, 21, 25, 12, 12, 12, 12, 12, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 21, 21, 25, 25, 75] 150 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]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 726) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 727) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298441 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 Building ZINC000416298441 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298441 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 724) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 7, 7, 7, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 12, 21, 25, 12, 12, 12, 12, 12, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 21, 21, 25, 25, 75] 150 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]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 725) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 7, 7, 7, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 12, 21, 25, 12, 12, 12, 12, 12, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 21, 21, 25, 25, 75] 150 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]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 726) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 727) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298441 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 Building ZINC000416298441 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298441 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 724) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 7, 7, 7, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 12, 21, 25, 12, 12, 12, 12, 12, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 21, 21, 25, 25, 75] 150 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]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 725) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 7, 7, 7, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 12, 21, 25, 12, 12, 12, 12, 12, 7, 10, 10, 7, 10, 10, 7, 12, 12, 12, 12, 12, 21, 21, 25, 25, 75] 150 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]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 726) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 727) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO) `ZINC000416298441.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000416298441 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@H](C)CN1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 5, 2, 7, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 9, 16, 20, 9, 9, 9, 9, 9, 6, 13, 13, 6, 13, 13, 6, 9, 9, 9, 9, 9, 16, 16, 20, 20, 60] 150 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]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298441 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298441 Building ZINC000416298442 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298442 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/728 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 18, 18, 22, 23, 18, 18, 18, 18, 13, 4, 13, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 22, 22, 23, 23, 69, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/729 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 18, 18, 22, 23, 18, 18, 18, 18, 13, 4, 13, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 22, 22, 23, 23, 69, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/730 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/730' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 13, 13, 13, 13, 18, 22, 13, 13, 13, 13, 10, 3, 10, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 13, 13, 13, 13, 13, 18, 18, 22, 22, 66, 13, 13, 13, 13, 13, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/731 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/731' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 13, 13, 13, 13, 18, 22, 13, 13, 13, 13, 10, 3, 10, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 13, 13, 13, 13, 13, 18, 18, 22, 22, 66, 13, 13, 13, 13, 13, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298442 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 Building ZINC000416298442 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298442 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 728) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 18, 18, 22, 23, 18, 18, 18, 18, 13, 4, 13, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 22, 22, 23, 23, 69, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 729) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 18, 18, 22, 23, 18, 18, 18, 18, 13, 4, 13, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 22, 22, 23, 23, 69, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 730) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 13, 13, 13, 13, 18, 22, 13, 13, 13, 13, 10, 3, 10, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 13, 13, 13, 13, 13, 18, 18, 22, 22, 66, 13, 13, 13, 13, 13, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 731) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 13, 13, 13, 13, 18, 22, 13, 13, 13, 13, 10, 3, 10, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 13, 13, 13, 13, 13, 18, 18, 22, 22, 66, 13, 13, 13, 13, 13, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298442 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 Building ZINC000416298442 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298442 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 728) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 18, 18, 22, 23, 18, 18, 18, 18, 13, 4, 13, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 22, 22, 23, 23, 69, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 729) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 18, 18, 22, 23, 18, 18, 18, 18, 13, 4, 13, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 22, 22, 23, 23, 69, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 730) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 13, 13, 13, 13, 18, 22, 13, 13, 13, 13, 10, 3, 10, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 13, 13, 13, 13, 13, 18, 18, 22, 22, 66, 13, 13, 13, 13, 13, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 731) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 13, 13, 13, 13, 18, 22, 13, 13, 13, 13, 10, 3, 10, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 13, 13, 13, 13, 13, 18, 18, 22, 22, 66, 13, 13, 13, 13, 13, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298442 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 Building ZINC000416298442 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000416298442 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 728) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 18, 18, 22, 23, 18, 18, 18, 18, 13, 4, 13, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 22, 22, 23, 23, 69, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 729) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 18, 18, 22, 23, 18, 18, 18, 18, 13, 4, 13, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 18, 18, 18, 18, 18, 22, 22, 23, 23, 69, 18, 18, 18, 18, 18, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 730) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 13, 13, 13, 13, 18, 22, 13, 13, 13, 13, 10, 3, 10, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 13, 13, 13, 13, 13, 18, 18, 22, 22, 66, 13, 13, 13, 13, 13, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 731) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000416298442.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000416298442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000416298442 none C[C@@H]1CN(CCO)[C@@H](C)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 10, 5, 5, 12, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 13, 13, 13, 13, 18, 22, 13, 13, 13, 13, 10, 3, 10, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 13, 13, 13, 13, 13, 18, 18, 22, 22, 66, 13, 13, 13, 13, 13, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000416298442 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000416298442 Building ZINC001702152087 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702152087 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/732 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001702152087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702152087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702152087 none CC[C@@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 42, 23, 42, 42, 50, 50, 50, 9, 23, 9, 9, 9, 9, 9, 9, 6, 1, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/733 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001702152087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702152087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702152087 none CC[C@@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 41, 18, 41, 41, 50, 50, 50, 8, 18, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 268 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702152087 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087 Building ZINC001702152087 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702152087 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 732) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001702152087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702152087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702152087 none CC[C@@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 42, 23, 42, 42, 50, 50, 50, 9, 23, 9, 9, 9, 9, 9, 9, 6, 1, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 733) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001702152087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702152087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702152087 none CC[C@@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 41, 18, 41, 41, 50, 50, 50, 8, 18, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 268 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702152087 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152087 Building ZINC001702152088 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702152088 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/734 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001702152088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702152088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702152088 none CC[C@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 40, 19, 40, 40, 50, 50, 50, 7, 19, 7, 7, 7, 7, 7, 7, 3, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/735 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001702152088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702152088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702152088 none CC[C@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 18, 37, 37, 50, 50, 50, 8, 18, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 49, 49, 49, 49, 49, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702152088 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088 Building ZINC001702152088 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702152088 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 734) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001702152088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702152088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702152088 none CC[C@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 40, 19, 40, 40, 50, 50, 50, 7, 19, 7, 7, 7, 7, 7, 7, 3, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 735) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001702152088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702152088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702152088 none CC[C@H](NC(C)=O)C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 18, 37, 37, 50, 50, 50, 8, 18, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 49, 49, 49, 49, 49, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702152088 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702152088 Building ZINC001281688456 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281688456 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/736 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COC2CCCCC2)C1) `ZINC001281688456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281688456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281688456 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COC2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 17, 42, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 7, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/737 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COC2CCCCC2)C1) `ZINC001281688456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281688456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281688456 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COC2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 20, 41, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 9, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281688456 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456 Building ZINC001281688456 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281688456 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 736) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COC2CCCCC2)C1) `ZINC001281688456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281688456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281688456 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COC2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 17, 42, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 7, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 737) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COC2CCCCC2)C1) `ZINC001281688456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281688456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001281688456 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COC2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 20, 41, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 9, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281688456 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281688456 Building ZINC001702166661 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166661 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/738 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001702166661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702166661 none CC(C)(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 8, 22, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/739 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001702166661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702166661 none CC(C)(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166661 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661 Building ZINC001702166661 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166661 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 738) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001702166661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702166661 none CC(C)(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 8, 22, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 739) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001702166661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702166661 none CC(C)(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166661 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166661 Building ZINC001702166673 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166673 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/740 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1ccccc1) `ZINC001702166673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166673 none CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 24, 46, 9, 24, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 46, 50, 50, 46, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 46, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/741 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1ccccc1) `ZINC001702166673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166673 none CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 21, 47, 8, 21, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 47, 50, 50, 47, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 47, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 212 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166673 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673 Building ZINC001702166673 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166673 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 740) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1ccccc1) `ZINC001702166673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166673 none CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 24, 46, 9, 24, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 46, 50, 50, 46, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 46, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 741) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1ccccc1) `ZINC001702166673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166673 none CO[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 21, 47, 8, 21, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 47, 50, 50, 47, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 47, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 212 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166673 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166673 Building ZINC001702166687 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166687 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/742 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001702166687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702166687 none Cc1noc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 27, 16, 12, 5, 4, 5, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 27, 26, 17, 17, 12, 12, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [49, 40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/743 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001702166687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702166687 none Cc1noc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 27, 16, 13, 9, 8, 9, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 27, 27, 16, 16, 13, 13, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166687 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687 Building ZINC001702166687 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166687 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 742) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1noc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001702166687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702166687 none Cc1noc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 27, 16, 12, 5, 4, 5, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 27, 26, 17, 17, 12, 12, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [49, 40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 743) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1noc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001702166687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702166687 none Cc1noc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 27, 16, 13, 9, 8, 9, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 27, 27, 16, 16, 13, 13, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166687 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166687 Building ZINC001702166765 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166765 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/744 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1OCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702166765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166765 none Cc1ccccc1OCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 20, 6, 4, 6, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 20, 20, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/316102/xbz-8058115.52/working/building/ZINC001702166765 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/745 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1OCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702166765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166765 none Cc1ccccc1OCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 44, 19, 7, 6, 7, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 19, 19, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166765 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765 Building ZINC001702166765 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166765 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 744) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccccc1OCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702166765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166765 none Cc1ccccc1OCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 20, 6, 4, 6, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 20, 20, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/316102/xbz-8058115.52/working/building/ZINC001702166765 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 745) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccccc1OCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702166765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166765 none Cc1ccccc1OCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 44, 19, 7, 6, 7, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 19, 19, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166765 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166765 Building ZINC001702166779 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166779 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/746 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H](F)Cc2ccccc2)C[C@H]1O) `ZINC001702166779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702166779 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H](F)Cc2ccccc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 21, 21, 42, 42, 42, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/747 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H](F)Cc2ccccc2)C[C@H]1O) `ZINC001702166779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702166779 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H](F)Cc2ccccc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 21, 21, 43, 43, 43, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166779 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779 Building ZINC001702166779 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166779 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 746) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H](F)Cc2ccccc2)C[C@H]1O) `ZINC001702166779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702166779 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H](F)Cc2ccccc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 21, 21, 42, 42, 42, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 747) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H](F)Cc2ccccc2)C[C@H]1O) `ZINC001702166779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702166779 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H](F)Cc2ccccc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 21, 21, 43, 43, 43, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166779 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166779 Building ZINC001702166780 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166780 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/748 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H](F)Cc2ccccc2)C[C@H]1O) `ZINC001702166780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702166780 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H](F)Cc2ccccc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 22, 22, 43, 43, 43, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/749 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H](F)Cc2ccccc2)C[C@H]1O) `ZINC001702166780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702166780 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H](F)Cc2ccccc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 24, 24, 42, 42, 42, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166780 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780 Building ZINC001702166780 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166780 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 748) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H](F)Cc2ccccc2)C[C@H]1O) `ZINC001702166780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702166780 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H](F)Cc2ccccc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 22, 22, 43, 43, 43, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 749) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H](F)Cc2ccccc2)C[C@H]1O) `ZINC001702166780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702166780 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H](F)Cc2ccccc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 24, 24, 42, 42, 42, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166780 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166780 Building ZINC001702166794 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166794 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/750 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccc(F)cc2)C[C@H]1O) `ZINC001702166794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702166794 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccc(F)cc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 16, 16, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/751 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccc(F)cc2)C[C@H]1O) `ZINC001702166794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702166794 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccc(F)cc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 16, 16, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166794 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794 Building ZINC001702166794 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166794 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 750) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccc(F)cc2)C[C@H]1O) `ZINC001702166794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702166794 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccc(F)cc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 16, 16, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 751) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccc(F)cc2)C[C@H]1O) `ZINC001702166794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702166794 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cc2ccc(F)cc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 16, 16, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166794 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166794 Building ZINC001702166879 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166879 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/752 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3cc[nH]c3c2)C[C@H]1O) `ZINC001702166879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702166879 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3cc[nH]c3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/753 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3cc[nH]c3c2)C[C@H]1O) `ZINC001702166879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702166879 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3cc[nH]c3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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/316102/xbz-8058115.52/working/building/ZINC001702166879 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166879 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879 Building ZINC001702166879 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166879 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 752) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3cc[nH]c3c2)C[C@H]1O) `ZINC001702166879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702166879 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3cc[nH]c3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 753) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3cc[nH]c3c2)C[C@H]1O) `ZINC001702166879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702166879 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3cc[nH]c3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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/316102/xbz-8058115.52/working/building/ZINC001702166879 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166879 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166879 Building ZINC001702166906 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166906 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/754 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccc(O)nc2)C[C@H]1O) `ZINC001702166906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702166906 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccc(O)nc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 21, 21, 33, 33, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 33, 33, 33, 33, 50, 50, 100, 50, 11, 11, 33] 300 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 290 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/755 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccc(O)nc2)C[C@H]1O) `ZINC001702166906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702166906 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccc(O)nc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 17, 17, 34, 34, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 34, 34, 34, 34, 50, 50, 100, 50, 10, 10, 30] 300 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166906 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906 Building ZINC001702166906 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166906 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 754) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccc(O)nc2)C[C@H]1O) `ZINC001702166906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702166906 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccc(O)nc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 21, 21, 33, 33, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 33, 33, 33, 33, 50, 50, 100, 50, 11, 11, 33] 300 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 290 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 755) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccc(O)nc2)C[C@H]1O) `ZINC001702166906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702166906 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCc2ccc(O)nc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 17, 17, 34, 34, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 34, 34, 34, 34, 50, 50, 100, 50, 10, 10, 30] 300 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166906 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166906 Building ZINC001702166907 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166907 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/756 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001702166907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702166907 none CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 11, 22, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/757 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/757' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001702166907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702166907 none CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 12, 22, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166907 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907 Building ZINC001702166907 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166907 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 756) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001702166907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702166907 none CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 11, 22, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 757) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001702166907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702166907 none CN(C)c1ccc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 12, 22, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166907 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166907 Building ZINC001702166917 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166917 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/758 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1) `ZINC001702166917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702166917 none CC(C)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 39, 50, 33, 39, 10, 33, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 239 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/759 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1) `ZINC001702166917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702166917 none CC(C)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 50, 31, 40, 8, 31, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 237 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166917 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917 Building ZINC001702166917 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166917 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 758) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1) `ZINC001702166917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702166917 none CC(C)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 39, 50, 33, 39, 10, 33, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 239 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 759) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1) `ZINC001702166917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702166917 none CC(C)[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 50, 31, 40, 8, 31, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 237 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166917 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166917 Building ZINC001702166918 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166918 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/760 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1) `ZINC001702166918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702166918 none CC(C)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 39, 50, 32, 39, 11, 32, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 242 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/761 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1) `ZINC001702166918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702166918 none CC(C)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 39, 50, 31, 39, 10, 31, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 237 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166918 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918 Building ZINC001702166918 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166918 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 760) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1) `ZINC001702166918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702166918 none CC(C)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 39, 50, 32, 39, 11, 32, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 242 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 761) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1) `ZINC001702166918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702166918 none CC(C)[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 39, 50, 31, 39, 10, 31, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 237 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166918 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166918 Building ZINC001702166950 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166950 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/762 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3c([nH]2)CCCC3)C[C@H]1O) `ZINC001702166950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702166950 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3c([nH]2)CCCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 18, 18, 18, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/763 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3c([nH]2)CCCC3)C[C@H]1O) `ZINC001702166950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702166950 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3c([nH]2)CCCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166950 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950 Building ZINC001702166950 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166950 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 762) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3c([nH]2)CCCC3)C[C@H]1O) `ZINC001702166950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702166950 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3c([nH]2)CCCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 18, 18, 18, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 763) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3c([nH]2)CCCC3)C[C@H]1O) `ZINC001702166950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702166950 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3c([nH]2)CCCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166950 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166950 Building ZINC001702166967 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166967 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/764 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001702166967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702166967 none Cc1ccc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 29, 27, 11, 7, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 29, 29, 27, 27, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/765 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001702166967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702166967 none Cc1ccc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 28, 28, 13, 10, 13, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166967 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967 Building ZINC001702166967 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166967 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 764) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001702166967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702166967 none Cc1ccc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 29, 27, 11, 7, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 29, 29, 27, 27, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 765) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001702166967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702166967 none Cc1ccc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 28, 28, 13, 10, 13, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166967 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166967 Building ZINC001702166984 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166984 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/766 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2Cc3ccccc3C2)C[C@H]1O) `ZINC001702166984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166984 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2Cc3ccccc3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 20, 28, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/767 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2Cc3ccccc3C2)C[C@H]1O) `ZINC001702166984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166984 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2Cc3ccccc3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 21, 29, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166984 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984 Building ZINC001702166984 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166984 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 766) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2Cc3ccccc3C2)C[C@H]1O) `ZINC001702166984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166984 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2Cc3ccccc3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 20, 28, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 767) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2Cc3ccccc3C2)C[C@H]1O) `ZINC001702166984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166984 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2Cc3ccccc3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 21, 29, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166984 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166984 Building ZINC001702166986 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166986 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/768 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C2CC2)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702166986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166986 none Cn1nc(C2CC2)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 42, 50, 50, 42, 20, 10, 20, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 42, 42, 42, 50, 50, 50, 50, 50, 42, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/769 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C2CC2)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702166986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166986 none Cn1nc(C2CC2)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 50, 50, 45, 18, 7, 18, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 45, 45, 45, 50, 50, 50, 50, 50, 45, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166986 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986 Building ZINC001702166986 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166986 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 768) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1nc(C2CC2)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702166986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166986 none Cn1nc(C2CC2)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 42, 50, 50, 42, 20, 10, 20, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 42, 42, 42, 50, 50, 50, 50, 50, 42, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 769) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cn1nc(C2CC2)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702166986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702166986 none Cn1nc(C2CC2)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 50, 50, 45, 18, 7, 18, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 45, 45, 45, 50, 50, 50, 50, 50, 45, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166986 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166986 Building ZINC001702166996 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166996 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/770 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001702166996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001702166996 none Cc1cc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 33, 31, 13, 7, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 33, 33, 31, 31, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/771 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001702166996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001702166996 none Cc1cc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 32, 31, 13, 8, 13, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 32, 32, 31, 31, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166996 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996 Building ZINC001702166996 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166996 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 770) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1cc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001702166996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001702166996 none Cc1cc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 33, 31, 13, 7, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 33, 33, 31, 31, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 771) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1cc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001702166996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001702166996 none Cc1cc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 32, 31, 13, 8, 13, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 32, 32, 31, 31, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166996 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166996 Building ZINC001702166997 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166997 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/772 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3c(s2)CCC3)C[C@H]1O) `ZINC001702166997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702166997 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3c(s2)CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 14, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/773 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3c(s2)CCC3)C[C@H]1O) `ZINC001702166997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702166997 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3c(s2)CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 14, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166997 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997 Building ZINC001702166997 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702166997 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 772) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3c(s2)CCC3)C[C@H]1O) `ZINC001702166997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702166997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702166997 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3c(s2)CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 14, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 773) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3c(s2)CCC3)C[C@H]1O) `ZINC001702166997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702166997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702166997 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3c(s2)CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 14, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702166997 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702166997 Building ZINC001702167001 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167001 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/774 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nccnc32)C[C@H]1O) `ZINC001702167001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001702167001 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nccnc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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/316102/xbz-8058115.52/working/building/ZINC001702167001 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/775 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nccnc32)C[C@H]1O) `ZINC001702167001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001702167001 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nccnc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167001 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001 Building ZINC001702167001 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167001 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 774) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nccnc32)C[C@H]1O) `ZINC001702167001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001702167001 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nccnc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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/316102/xbz-8058115.52/working/building/ZINC001702167001 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 775) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nccnc32)C[C@H]1O) `ZINC001702167001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001702167001 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nccnc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167001 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167001 Building ZINC001702167003 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167003 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/776 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1) `ZINC001702167003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702167003 none C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 39, 46, 14, 7, 14, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 46, 50, 50, 50, 50, 46, 46, 46, 39, 39, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/777 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1) `ZINC001702167003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702167003 none C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 39, 46, 16, 9, 16, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 46, 50, 50, 50, 50, 46, 46, 46, 39, 39, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167003 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003 Building ZINC001702167003 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167003 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 776) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1) `ZINC001702167003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702167003 none C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 39, 46, 14, 7, 14, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 46, 50, 50, 50, 50, 46, 46, 46, 39, 39, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 777) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1) `ZINC001702167003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702167003 none C[C@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 39, 46, 16, 9, 16, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 46, 50, 50, 50, 50, 46, 46, 46, 39, 39, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167003 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167003 Building ZINC001702167004 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167004 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/778 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1) `ZINC001702167004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702167004 none C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 37, 44, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 44, 50, 50, 50, 50, 44, 44, 44, 37, 37, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/779 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1) `ZINC001702167004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702167004 none C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 39, 45, 16, 10, 16, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 45, 50, 50, 50, 50, 45, 45, 45, 39, 39, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167004 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004 Building ZINC001702167004 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167004 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 778) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1) `ZINC001702167004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702167004 none C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 37, 44, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 44, 50, 50, 50, 50, 44, 44, 44, 37, 37, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 779) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1) `ZINC001702167004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702167004 none C[C@@H](CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 39, 45, 16, 10, 16, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 45, 50, 50, 50, 50, 45, 45, 45, 39, 39, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167004 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167004 Building ZINC001702167021 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167021 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/780 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@H]1O) `ZINC001702167021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702167021 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'F', 'F', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 15, 15, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 25, 25, 46, 46, 46, 46, 50, 50, 46, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 46, 46, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/781 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@H]1O) `ZINC001702167021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702167021 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'F', 'F', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 15, 15, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 23, 23, 42, 42, 42, 42, 50, 50, 42, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 42, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167021 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021 Building ZINC001702167021 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167021 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 780) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@H]1O) `ZINC001702167021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702167021 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'F', 'F', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 15, 15, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 25, 25, 46, 46, 46, 46, 50, 50, 46, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 46, 46, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 781) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@H]1O) `ZINC001702167021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702167021 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn(C(F)F)n2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'F', 'F', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 15, 15, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 23, 23, 42, 42, 42, 42, 50, 50, 42, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 42, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167021 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167021 Building ZINC001702167880 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167880 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/782 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cccnc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167880 none CCOc1cccnc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 36, 36, 36, 36, 36, 36, 13, 11, 13, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 36, 36, 36, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/783 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cccnc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167880 none CCOc1cccnc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 33, 33, 33, 33, 33, 33, 12, 11, 12, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 33, 33, 33, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167880 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880 Building ZINC001702167880 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167880 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 782) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOc1cccnc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167880 none CCOc1cccnc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 36, 36, 36, 36, 36, 36, 13, 11, 13, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 36, 36, 36, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 783) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCOc1cccnc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167880 none CCOc1cccnc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 33, 33, 33, 33, 33, 33, 12, 11, 12, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 33, 33, 33, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167880 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167880 Building ZINC001702167890 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167890 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/784 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1oncc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167890 none CC(C)c1oncc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 24, 9, 24, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 133 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/785 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1oncc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167890 none CC(C)c1oncc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 21, 7, 21, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 123 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167890 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890 Building ZINC001702167890 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167890 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 784) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)c1oncc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167890 none CC(C)c1oncc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 24, 9, 24, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 133 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 785) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)c1oncc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167890 none CC(C)c1oncc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 21, 7, 21, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 123 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167890 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167890 Building ZINC001702167972 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702167972 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/786 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 50, 11, 8, 11, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/787 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 50, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/788 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/788' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 50, 11, 8, 11, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/789 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/789' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 50, 10, 6, 10, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50] 150 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56, 57]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167972 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 Building ZINC001702167972 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702167972 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 786) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 50, 11, 8, 11, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 787) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 50, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 788) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 50, 11, 8, 11, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 789) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 50, 10, 6, 10, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50] 150 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56, 57]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167972 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 Building ZINC001702167972 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702167972 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 786) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 50, 11, 8, 11, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 787) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 50, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 788) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 50, 11, 8, 11, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 789) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 50, 10, 6, 10, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50] 150 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56, 57]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167972 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 Building ZINC001702167972 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702167972 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 786) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 50, 11, 8, 11, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 787) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 50, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 788) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 50, 11, 8, 11, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 150 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56, 57]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 789) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702167972.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702167972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167972 none CO[C@H]1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 50, 10, 6, 10, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50] 150 rigid atoms, others: [51, 50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56, 57]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167972 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167972 Building ZINC001702167171 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167171 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/790 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Cl)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1C) `ZINC001702167171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702167171 none Cc1c(Cl)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 24, 11, 24, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/316102/xbz-8058115.52/working/building/ZINC001702167171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/791 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Cl)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1C) `ZINC001702167171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702167171 none Cc1c(Cl)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 27, 12, 27, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167171 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171 Building ZINC001702167171 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167171 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 790) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1c(Cl)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1C) `ZINC001702167171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702167171 none Cc1c(Cl)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 24, 11, 24, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/316102/xbz-8058115.52/working/building/ZINC001702167171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 791) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1c(Cl)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1C) `ZINC001702167171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702167171 none Cc1c(Cl)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 27, 12, 27, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167171 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167171 Building ZINC001702167185 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167185 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/792 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3c4ccccc4C[C@H]23)C[C@H]1O) `ZINC001702167185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167185 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3c4ccccc4C[C@H]23)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 34, 3, 32, 37, 38, 33, 40, 39, 2, 35, 4, 6, 5, 36] set([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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/793 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3c4ccccc4C[C@H]23)C[C@H]1O) `ZINC001702167185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167185 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3c4ccccc4C[C@H]23)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 34, 3, 32, 37, 38, 33, 40, 39, 2, 35, 4, 6, 5, 36] set([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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167185 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185 Building ZINC001702167185 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167185 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 792) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3c4ccccc4C[C@H]23)C[C@H]1O) `ZINC001702167185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167185 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3c4ccccc4C[C@H]23)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 34, 3, 32, 37, 38, 33, 40, 39, 2, 35, 4, 6, 5, 36] set([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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 793) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3c4ccccc4C[C@H]23)C[C@H]1O) `ZINC001702167185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167185 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2[C@@H]3c4ccccc4C[C@H]23)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 34, 3, 32, 37, 38, 33, 40, 39, 2, 35, 4, 6, 5, 36] set([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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167185 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167185 Building ZINC001702167186 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167186 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/794 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2[C@@H]3Cc4ccccc4[C@@H]32)C[C@H]1O) `ZINC001702167186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167186 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2[C@@H]3Cc4ccccc4[C@@H]32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 34, 3, 32, 37, 38, 33, 40, 39, 2, 35, 4, 6, 5, 36] set([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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/795 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2[C@@H]3Cc4ccccc4[C@@H]32)C[C@H]1O) `ZINC001702167186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167186 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2[C@@H]3Cc4ccccc4[C@@H]32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 34, 3, 32, 37, 38, 33, 40, 39, 2, 35, 4, 6, 5, 36] set([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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167186 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186 Building ZINC001702167186 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167186 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 794) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2[C@@H]3Cc4ccccc4[C@@H]32)C[C@H]1O) `ZINC001702167186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167186 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2[C@@H]3Cc4ccccc4[C@@H]32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 34, 3, 32, 37, 38, 33, 40, 39, 2, 35, 4, 6, 5, 36] set([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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 795) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2[C@@H]3Cc4ccccc4[C@@H]32)C[C@H]1O) `ZINC001702167186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 Warning: atom stereo specified for planar atom 19 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167186 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2[C@@H]3Cc4ccccc4[C@@H]32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 34, 3, 32, 37, 38, 33, 40, 39, 2, 35, 4, 6, 5, 36] set([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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167186 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167186 Building ZINC001702167194 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167194 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/796 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167194 none CCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 12, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 44, 44, 44, 44, 44, 19, 7, 19, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 44, 44, 44, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/797 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167194 none CCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 12, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 42, 42, 42, 42, 42, 20, 10, 20, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 42, 42, 42, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167194 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194 Building ZINC001702167194 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167194 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 796) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167194 none CCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 12, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 44, 44, 44, 44, 44, 19, 7, 19, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 44, 44, 44, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 797) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167194 none CCc1onc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 12, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 42, 42, 42, 42, 42, 20, 10, 20, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 42, 42, 42, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167194 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167194 Building ZINC001702167195 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167195 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/798 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnn(C(F)F)c2)C[C@H]1O) `ZINC001702167195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702167195 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnn(C(F)F)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 15, 15, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 19, 19, 42, 42, 42, 42, 50, 50, 42, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 50, 42, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/799 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnn(C(F)F)c2)C[C@H]1O) `ZINC001702167195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702167195 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnn(C(F)F)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 15, 15, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 18, 18, 43, 43, 43, 43, 50, 50, 43, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 43, 50, 43, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167195 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195 Building ZINC001702167195 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167195 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 798) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnn(C(F)F)c2)C[C@H]1O) `ZINC001702167195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702167195 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnn(C(F)F)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 15, 15, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 19, 19, 42, 42, 42, 42, 50, 50, 42, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 50, 42, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 799) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnn(C(F)F)c2)C[C@H]1O) `ZINC001702167195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702167195 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnn(C(F)F)c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 15, 15, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 18, 18, 43, 43, 43, 43, 50, 50, 43, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 43, 50, 43, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167195 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167195 Building ZINC001702167219 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167219 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/800 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@H]1O) `ZINC001702167219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001702167219 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/801 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@H]1O) `ZINC001702167219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001702167219 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167219 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219 Building ZINC001702167219 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167219 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 800) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@H]1O) `ZINC001702167219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001702167219 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 801) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@H]1O) `ZINC001702167219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001702167219 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc3ccccc3nn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167219 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167219 Building ZINC001702167226 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167226 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/802 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCCC1) `ZINC001702167226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167226 none COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 44, 36, 36, 14, 36, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 36, 36, 36, 36, 50, 50, 50, 50, 50, 44, 44, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 36, 36, 36, 36, 36, 36, 36, 36] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 224 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/803 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCCC1) `ZINC001702167226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167226 none COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 38, 35, 15, 35, 15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 38, 38, 38, 38, 50, 50, 50, 50, 50, 42, 42, 15, 15, 45, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 225 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167226 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226 Building ZINC001702167226 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167226 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 802) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCCC1) `ZINC001702167226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167226 none COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 44, 36, 36, 14, 36, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 36, 36, 36, 36, 50, 50, 50, 50, 50, 44, 44, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 36, 36, 36, 36, 36, 36, 36, 36] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 224 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 803) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCCC1) `ZINC001702167226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702167226 none COCCC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 38, 35, 15, 35, 15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 38, 38, 38, 38, 50, 50, 50, 50, 50, 42, 42, 15, 15, 45, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 225 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167226 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167226 Building ZINC001702167235 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167235 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/804 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n[nH]1) `ZINC001702167235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702167235 none CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 39, 50, 39, 39, 23, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 39, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/805 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n[nH]1) `ZINC001702167235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702167235 none CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 50, 40, 40, 23, 11, 23, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 40, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167235 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235 Building ZINC001702167235 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167235 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 804) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n[nH]1) `ZINC001702167235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702167235 none CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 39, 50, 39, 39, 23, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 39, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 805) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n[nH]1) `ZINC001702167235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702167235 none CC(C)c1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 50, 40, 40, 23, 11, 23, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 40, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167235 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167235 Building ZINC001702167240 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167240 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/806 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167240 none Cc1nn(C)c(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/316102/xbz-8058115.52/working/building/ZINC001702167240 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/807 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167240 none Cc1nn(C)c(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 12, 30, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167240 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240 Building ZINC001702167240 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167240 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 806) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167240 none Cc1nn(C)c(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/316102/xbz-8058115.52/working/building/ZINC001702167240 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 807) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C)c(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001702167240 none Cc1nn(C)c(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 12, 30, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167240 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167240 Building ZINC001702167249 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167249 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/808 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)s1) `ZINC001702167249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702167249 none Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 28, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/809 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)s1) `ZINC001702167249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702167249 none Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167249 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249 Building ZINC001702167249 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167249 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 808) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)s1) `ZINC001702167249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702167249 none Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 28, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 809) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)s1) `ZINC001702167249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702167249 none Cc1nc(C)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167249 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167249 Building ZINC001702167364 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167364 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/810 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(F)ccc2F)C[C@H]1O) `ZINC001702167364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702167364 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(F)ccc2F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 23, 23, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/811 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(F)ccc2F)C[C@H]1O) `ZINC001702167364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702167364 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(F)ccc2F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 24, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167364 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364 Building ZINC001702167364 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167364 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 810) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(F)ccc2F)C[C@H]1O) `ZINC001702167364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702167364 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(F)ccc2F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 23, 23, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 811) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(F)ccc2F)C[C@H]1O) `ZINC001702167364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702167364 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cc(F)ccc2F)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 24, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167364 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167364 Building ZINC001702167367 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167367 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/812 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001702167367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167367 none Cc1cnc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 33, 19, 15, 7, 4, 7, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 32, 32, 21, 21, 15, 15, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [50, 49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/813 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001702167367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167367 none Cc1cnc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 31, 18, 15, 10, 8, 10, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 31, 31, 18, 18, 15, 15, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167367 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367 Building ZINC001702167367 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167367 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 812) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1cnc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001702167367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167367 none Cc1cnc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 33, 19, 15, 7, 4, 7, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 32, 32, 21, 21, 15, 15, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [50, 49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 813) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1cnc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001702167367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167367 none Cc1cnc(CCCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 31, 18, 15, 10, 8, 10, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 31, 31, 18, 18, 15, 15, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167367 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167367 Building ZINC001702167459 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167459 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/814 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(Cl)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001702167459 none Cc1noc(Cl)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 16, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 7, 11, 7, 7, 7, 7, 7, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 30, 30, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/815 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(Cl)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001702167459 none Cc1noc(Cl)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 16, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 7, 11, 7, 7, 7, 7, 7, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 30, 30, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167459 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459 Building ZINC001702167459 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167459 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 814) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1noc(Cl)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001702167459 none Cc1noc(Cl)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 16, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 7, 11, 7, 7, 7, 7, 7, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 30, 30, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 815) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1noc(Cl)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001702167459 none Cc1noc(Cl)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 16, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 7, 11, 7, 7, 7, 7, 7, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 30, 30, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167459 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167459 Building ZINC001702167527 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167527 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/816 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167527 none CN(C)c1ccccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 44, 50, 50, 28, 13, 28, 13, 13, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 185 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/817 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167527 none CN(C)c1ccccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 44, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 169 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167527 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527 Building ZINC001702167527 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702167527 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 816) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)c1ccccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702167527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167527 none CN(C)c1ccccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 44, 50, 50, 28, 13, 28, 13, 13, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 185 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 817) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)c1ccccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702167527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702167527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001702167527 none CN(C)c1ccccc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 44, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 169 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702167527 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702167527 Building ZINC001702175218 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702175218 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/818 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2cccs2)C1) `ZINC001702175218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702175218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702175218 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2cccs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 35, 39, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 10, 35, 35, 39, 39, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/819 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2cccs2)C1) `ZINC001702175218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702175218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702175218 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2cccs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 31, 34, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 10, 31, 31, 34, 34, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702175218 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218 Building ZINC001702175218 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702175218 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 818) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2cccs2)C1) `ZINC001702175218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702175218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702175218 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2cccs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 35, 39, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 10, 35, 35, 39, 39, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 819) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2cccs2)C1) `ZINC001702175218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702175218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702175218 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCc2cccs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 31, 34, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 10, 31, 31, 34, 34, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702175218 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702175218 Building ZINC001702176528 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702176528 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/820 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCOc2ccccc2)C1) `ZINC001702176528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702176528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702176528 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCOc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 29, 35, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 5, 29, 29, 35, 35, 50, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/821 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCOc2ccccc2)C1) `ZINC001702176528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702176528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702176528 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCOc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 25, 33, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 5, 25, 25, 33, 33, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702176528 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528 Building ZINC001702176528 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702176528 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 820) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCOc2ccccc2)C1) `ZINC001702176528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702176528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702176528 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCOc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 29, 35, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 5, 29, 29, 35, 35, 50, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 821) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCOc2ccccc2)C1) `ZINC001702176528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702176528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702176528 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCOc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 25, 33, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 5, 25, 25, 33, 33, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702176528 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176528 Building ZINC001702176899 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702176899 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/822 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COc2ccccc2F)C1) `ZINC001702176899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702176899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001702176899 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COc2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.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', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 41, 50, 50, 47, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 17, 17, 50, 50, 50, 50, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48] set([39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/823 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COc2ccccc2F)C1) `ZINC001702176899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702176899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001702176899 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COc2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.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', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 19, 40, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 5, 19, 19, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702176899 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899 Building ZINC001702176899 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702176899 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 822) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COc2ccccc2F)C1) `ZINC001702176899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702176899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001702176899 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COc2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.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', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 41, 50, 50, 47, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 17, 17, 50, 50, 50, 50, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48] set([39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 823) grep: /scratch/xiaobo/316102/xbz-8058115.52/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)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COc2ccccc2F)C1) `ZINC001702176899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702176899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001702176899 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)COc2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.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', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 19, 40, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 5, 19, 19, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702176899 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702176899 Building ZINC001702187190 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702187190 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/824 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCCCC1) `ZINC001702187190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702187190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702187190 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 28, 17, 17, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 40, 40, 40, 40, 40, 50, 50, 50, 50, 50, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/825 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCCCC1) `ZINC001702187190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702187190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702187190 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 25, 19, 19, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 43, 43, 43, 43, 43, 50, 50, 50, 50, 50, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702187190 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190 Building ZINC001702187190 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702187190 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 824) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCCCC1) `ZINC001702187190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702187190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702187190 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 28, 17, 17, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 40, 40, 40, 40, 40, 50, 50, 50, 50, 50, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 825) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCCCC1) `ZINC001702187190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702187190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702187190 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 25, 19, 19, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 43, 43, 43, 43, 43, 50, 50, 50, 50, 50, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702187190 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702187190 Building ZINC001702190317 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702190317 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/826 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 7, 7, 7, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/827 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/828 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/828' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 49, 50, 24, 9, 9, 9, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/829 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/829' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 49, 50, 23, 8, 8, 8, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702190317 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 Building ZINC001702190317 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702190317 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 826) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 7, 7, 7, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 827) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 828) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 49, 50, 24, 9, 9, 9, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 829) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 49, 50, 23, 8, 8, 8, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702190317 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 Building ZINC001702190317 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702190317 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 826) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 7, 7, 7, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 827) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 828) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 49, 50, 24, 9, 9, 9, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 829) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 49, 50, 23, 8, 8, 8, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702190317 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 Building ZINC001702190317 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702190317 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 826) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 7, 7, 7, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 827) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 50, 24, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 828) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 49, 50, 24, 9, 9, 9, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 829) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1) `ZINC001702190317.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702190317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702190317 none C[C@H]1CC[C@@H](OCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 49, 50, 23, 8, 8, 8, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702190317 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702190317 Building ZINC001702198464 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702198464 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/830 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702198464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702198464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702198464 none CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 11, 33, 11, 11, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 33, 50, 50, 50, 50, 33, 33, 33, 33, 33, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/831 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702198464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702198464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702198464 none CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 14, 34, 14, 14, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 35, 50, 50, 50, 50, 34, 34, 34, 34, 34, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702198464 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464 Building ZINC001702198464 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702198464 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 830) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702198464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702198464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702198464 none CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 11, 33, 11, 11, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 33, 50, 50, 50, 50, 33, 33, 33, 33, 33, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 831) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702198464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702198464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702198464 none CCO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 14, 34, 14, 14, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 35, 50, 50, 50, 50, 34, 34, 34, 34, 34, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702198464 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198464 Building ZINC001702198465 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702198465 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/832 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702198465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702198465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702198465 none CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 31, 12, 31, 12, 12, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 34, 50, 50, 50, 50, 32, 32, 32, 32, 32, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/833 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702198465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702198465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702198465 none CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 37, 12, 37, 12, 12, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 40, 50, 50, 50, 50, 38, 38, 38, 38, 38, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702198465 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465 Building ZINC001702198465 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702198465 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 832) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702198465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702198465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702198465 none CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 31, 12, 31, 12, 12, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 34, 50, 50, 50, 50, 32, 32, 32, 32, 32, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 833) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702198465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702198465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001702198465 none CCO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 37, 12, 37, 12, 12, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 40, 50, 50, 50, 50, 38, 38, 38, 38, 38, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702198465 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198465 Building ZINC001702198057 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702198057 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/834 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1) `ZINC001702198057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702198057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702198057 none CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 16, 50, 16, 16, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/835 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1) `ZINC001702198057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702198057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702198057 none CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 14, 45, 14, 14, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 45, 50, 50, 46, 50, 50, 50, 50, 50, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 50, 50, 46, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702198057 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057 Building ZINC001702198057 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702198057 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 834) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1) `ZINC001702198057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702198057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702198057 none CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 16, 50, 16, 16, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 835) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1) `ZINC001702198057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702198057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702198057 none CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 14, 45, 14, 14, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 45, 50, 50, 46, 50, 50, 50, 50, 50, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 50, 50, 46, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702198057 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702198057 Building ZINC001702199825 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702199825 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/836 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001702199825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702199825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702199825 none CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 31, 23, 14, 5, 5, 5, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 14, 14, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [51, 50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/837 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001702199825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702199825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702199825 none CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 47, 46, 30, 22, 14, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 47, 47, 46, 46, 30, 30, 14, 14, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [51, 50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702199825 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825 Building ZINC001702199825 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702199825 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 836) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001702199825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702199825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702199825 none CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 31, 23, 14, 5, 5, 5, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 14, 14, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [51, 50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 837) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001702199825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702199825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702199825 none CCCCCCOCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 47, 46, 30, 22, 14, 7, 7, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 47, 47, 46, 46, 30, 30, 14, 14, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [51, 50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702199825 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702199825 Building ZINC001702201278 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702201278 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/838 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702201278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702201278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702201278 none CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 15, 34, 15, 15, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 35, 50, 50, 50, 50, 34, 34, 34, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/839 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702201278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702201278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702201278 none CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 16, 33, 16, 16, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 35, 50, 50, 50, 50, 33, 33, 33, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702201278 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278 Building ZINC001702201278 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702201278 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 838) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702201278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702201278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702201278 none CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 15, 34, 15, 15, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 35, 50, 50, 50, 50, 34, 34, 34, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 839) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702201278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702201278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702201278 none CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 16, 33, 16, 16, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 35, 50, 50, 50, 50, 33, 33, 33, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702201278 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201278 Building ZINC001702201279 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702201279 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/840 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702201279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702201279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702201279 none CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 15, 36, 15, 15, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 37, 50, 50, 50, 50, 36, 36, 36, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/841 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702201279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702201279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702201279 none CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 15, 32, 15, 15, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 34, 50, 50, 50, 50, 32, 32, 32, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702201279 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279 Building ZINC001702201279 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702201279 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 840) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702201279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702201279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702201279 none CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 15, 36, 15, 15, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 37, 50, 50, 50, 50, 36, 36, 36, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 841) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1) `ZINC001702201279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702201279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702201279 none CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 15, 32, 15, 15, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 34, 50, 50, 50, 50, 32, 32, 32, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702201279 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702201279 Building ZINC001702202892 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702202892 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/842 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1) `ZINC001702202892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702202892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001702202892 none Cc1csc(CCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 47, 24, 24, 24, 10, 10, 10, 10, 5, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 48, 48, 47, 47, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/843 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1) `ZINC001702202892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702202892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001702202892 none Cc1csc(CCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 45, 35, 15, 15, 15, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 45, 45, 35, 35, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 207 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702202892 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892 Building ZINC001702202892 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702202892 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 842) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1csc(CCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1) `ZINC001702202892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702202892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001702202892 none Cc1csc(CCC(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 47, 24, 24, 24, 10, 10, 10, 10, 5, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 48, 48, 47, 47, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 843) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1csc(CCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1) `ZINC001702202892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702202892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001702202892 none Cc1csc(CCC(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 45, 35, 15, 15, 15, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 45, 45, 35, 35, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 207 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702202892 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702202892 Building ZINC001343627713 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343627713 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/844 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(F)(F)F)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343627713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343627713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343627713 none C[C@H](CC(F)(F)F)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 15, 15, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 19, 41, 41, 50, 50, 50, 50, 19, 19, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 41, 41, 41, 50, 50, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/845 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(F)(F)F)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343627713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343627713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343627713 none C[C@H](CC(F)(F)F)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 15, 15, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 17, 40, 40, 50, 50, 50, 50, 17, 17, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 40, 40, 40, 50, 50, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343627713 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713 Building ZINC001343627713 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343627713 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 844) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](CC(F)(F)F)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343627713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343627713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343627713 none C[C@H](CC(F)(F)F)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 15, 15, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 19, 41, 41, 50, 50, 50, 50, 19, 19, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 41, 41, 41, 50, 50, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 845) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@H](CC(F)(F)F)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343627713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343627713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343627713 none C[C@H](CC(F)(F)F)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 15, 15, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 17, 40, 40, 50, 50, 50, 50, 17, 17, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 40, 40, 40, 50, 50, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343627713 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343627713 Building ZINC001702214502 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702214502 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/846 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC) `ZINC001702214502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702214502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702214502 none CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 28, 11, 28, 11, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 28, 41, 50, 41, 50, 36, 36, 36, 36, 36, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 317 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/847 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC) `ZINC001702214502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702214502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702214502 none CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 30, 13, 30, 13, 13, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 30, 40, 50, 40, 50, 38, 38, 38, 38, 38, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 329 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702214502 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502 Building ZINC001702214502 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702214502 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 846) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC) `ZINC001702214502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702214502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702214502 none CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 28, 11, 28, 11, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 28, 41, 50, 41, 50, 36, 36, 36, 36, 36, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 317 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 847) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC) `ZINC001702214502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702214502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702214502 none CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 30, 13, 30, 13, 13, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 30, 40, 50, 40, 50, 38, 38, 38, 38, 38, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 329 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702214502 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214502 Building ZINC001702214503 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702214503 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/848 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC) `ZINC001702214503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702214503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702214503 none CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 29, 11, 29, 11, 11, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 29, 38, 50, 38, 50, 36, 36, 36, 36, 36, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 335 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/849 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC) `ZINC001702214503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702214503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702214503 none CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 30, 10, 30, 10, 10, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 30, 41, 50, 41, 50, 39, 39, 39, 39, 39, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 327 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702214503 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503 Building ZINC001702214503 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702214503 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 848) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC) `ZINC001702214503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702214503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702214503 none CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 29, 11, 29, 11, 11, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 29, 38, 50, 38, 50, 36, 36, 36, 36, 36, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 335 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 849) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC) `ZINC001702214503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702214503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001702214503 none CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 30, 10, 30, 10, 10, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 30, 41, 50, 41, 50, 39, 39, 39, 39, 39, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 327 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702214503 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702214503 Building ZINC001702228930 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702228930 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/850 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(N)=O)C[C@H]1c1ccccc1F) `ZINC001702228930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702228930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702228930 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(N)=O)C[C@H]1c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 19, 19, 32, 32, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 32, 32, 10, 10, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/851 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(N)=O)C[C@H]1c1ccccc1F) `ZINC001702228930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702228930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702228930 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(N)=O)C[C@H]1c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 19, 19, 36, 36, 11, 11, 11, 11, 18, 18, 11, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 36, 36, 11, 11, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702228930 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930 Building ZINC001702228930 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702228930 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 850) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(N)=O)C[C@H]1c1ccccc1F) `ZINC001702228930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702228930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702228930 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(N)=O)C[C@H]1c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 19, 19, 32, 32, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 32, 32, 10, 10, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 851) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(N)=O)C[C@H]1c1ccccc1F) `ZINC001702228930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702228930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702228930 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(N)=O)C[C@H]1c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 19, 19, 36, 36, 11, 11, 11, 11, 18, 18, 11, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 36, 36, 11, 11, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702228930 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702228930 Building ZINC001343670366 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343670366 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/852 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CCOCC1) `ZINC001343670366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343670366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343670366 none CCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 27, 26, 26, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/853 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CCOCC1) `ZINC001343670366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343670366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343670366 none CCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 26, 22, 22, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 22, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 24, 49, 49, 49, 49, 49, 49, 49, 49] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343670366 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366 Building ZINC001343670366 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343670366 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 852) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CCOCC1) `ZINC001343670366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343670366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343670366 none CCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 27, 26, 26, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 853) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CCOCC1) `ZINC001343670366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343670366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001343670366 none CCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 26, 22, 22, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 22, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 24, 49, 49, 49, 49, 49, 49, 49, 49] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343670366 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343670366 Building ZINC001702239173 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702239173 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/854 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C)ncc1C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702239173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702239173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702239173 none COc1nc(C)ncc1C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 50, 50, 50, 31, 13, 31, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/855 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C)ncc1C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702239173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702239173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702239173 none COc1nc(C)ncc1C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 50, 50, 50, 29, 12, 29, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702239173 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173 Building ZINC001702239173 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702239173 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 854) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1nc(C)ncc1C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702239173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702239173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702239173 none COc1nc(C)ncc1C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 50, 50, 50, 31, 13, 31, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 855) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1nc(C)ncc1C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001702239173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702239173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702239173 none COc1nc(C)ncc1C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 50, 50, 50, 29, 12, 29, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702239173 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239173 Building ZINC001702239828 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702239828 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/856 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001702239828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702239828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001702239828 none CC(=O)N1CCC[C@@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 23, 49, 15, 23, 15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 49, 50, 50, 50, 49, 49, 49, 49, 49, 49, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 49, 49] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 153 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/857 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001702239828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702239828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001702239828 none CC(=O)N1CCC[C@@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 50, 13, 22, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 149 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702239828 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828 Building ZINC001702239828 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702239828 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 856) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001702239828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702239828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001702239828 none CC(=O)N1CCC[C@@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 23, 49, 15, 23, 15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 49, 50, 50, 50, 49, 49, 49, 49, 49, 49, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 49, 49] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 153 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 857) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001702239828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702239828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001702239828 none CC(=O)N1CCC[C@@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 50, 13, 22, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 149 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702239828 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239828 Building ZINC001702239834 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702239834 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/858 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001702239834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702239834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001702239834 none CC(=O)N1CCC[C@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 13, 23, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 149 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/859 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001702239834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702239834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001702239834 none CC(=O)N1CCC[C@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 14, 23, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 153 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702239834 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834 Building ZINC001702239834 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702239834 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 858) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(=O)N1CCC[C@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001702239834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702239834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001702239834 none CC(=O)N1CCC[C@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 13, 23, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 149 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 859) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(=O)N1CCC[C@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001702239834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702239834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001702239834 none CC(=O)N1CCC[C@H](C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 23, 50, 14, 23, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 153 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702239834 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239834 Building ZINC001702239918 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702239918 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/860 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(O)c(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C) `ZINC001702239918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702239918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702239918 none Cc1nnc(O)c(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 12, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 12, 32, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 100, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50] 100 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/861 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(O)c(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C) `ZINC001702239918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702239918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702239918 none Cc1nnc(O)c(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 12, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 13, 36, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 100, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50] 100 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702239918 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918 Building ZINC001702239918 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702239918 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 860) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(O)c(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C) `ZINC001702239918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702239918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702239918 none Cc1nnc(O)c(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 12, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 12, 32, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 100, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50] 100 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 861) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(O)c(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C) `ZINC001702239918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702239918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702239918 none Cc1nnc(O)c(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 12, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 13, 36, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 100, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50] 100 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702239918 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702239918 Building ZINC001281750006 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281750006 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/862 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001281750006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281750006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281750006 none CO[C@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 33, 18, 33, 10, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 33, 50, 50, 50, 50, 50, 35, 35, 35, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/863 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001281750006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281750006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281750006 none CO[C@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 36, 16, 36, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 36, 50, 50, 50, 50, 50, 39, 39, 39, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281750006 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006 Building ZINC001281750006 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281750006 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 862) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001281750006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281750006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281750006 none CO[C@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 33, 18, 33, 10, 18, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 33, 50, 50, 50, 50, 50, 35, 35, 35, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 863) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001281750006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281750006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281750006 none CO[C@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 36, 16, 36, 8, 16, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 36, 50, 50, 50, 50, 50, 39, 39, 39, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281750006 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750006 Building ZINC001281750007 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281750007 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/864 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001281750007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281750007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281750007 none CO[C@@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 29, 11, 18, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 29, 50, 50, 50, 50, 50, 30, 30, 30, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/865 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001281750007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281750007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281750007 none CO[C@@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 17, 30, 12, 17, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 30, 50, 50, 50, 50, 50, 31, 31, 31, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281750007 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007 Building ZINC001281750007 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281750007 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 864) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001281750007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281750007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281750007 none CO[C@@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 29, 11, 18, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 29, 50, 50, 50, 50, 50, 30, 30, 30, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 865) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001281750007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281750007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001281750007 none CO[C@@H](C(=O)N1C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 17, 30, 12, 17, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 30, 50, 50, 50, 50, 50, 31, 31, 31, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281750007 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750007 Building ZINC001281750435 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281750435 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/866 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)c2cccc(C(N)=O)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281750435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281750435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281750435 none C[C@@H]1CN(C(=O)c2cccc(C(N)=O)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 11, 11, 14, 14, 14, 20, 20, 44, 44, 44, 44, 44, 50, 50, 44, 14, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 44, 44, 44, 50, 50, 44, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/316102/xbz-8058115.52/working/building/ZINC001281750435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/867 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)c2cccc(C(N)=O)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281750435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281750435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281750435 none C[C@@H]1CN(C(=O)c2cccc(C(N)=O)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 13, 16, 16, 16, 22, 22, 44, 44, 44, 44, 44, 50, 50, 44, 16, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 44, 44, 44, 50, 50, 44, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/316102/xbz-8058115.52/working/building/ZINC001281750435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281750435 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435 Building ZINC001281750435 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281750435 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 866) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)c2cccc(C(N)=O)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281750435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281750435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281750435 none C[C@@H]1CN(C(=O)c2cccc(C(N)=O)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 11, 11, 14, 14, 14, 20, 20, 44, 44, 44, 44, 44, 50, 50, 44, 14, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 44, 44, 44, 50, 50, 44, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/316102/xbz-8058115.52/working/building/ZINC001281750435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 867) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: C[C@@H]1CN(C(=O)c2cccc(C(N)=O)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281750435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281750435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281750435 none C[C@@H]1CN(C(=O)c2cccc(C(N)=O)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 13, 16, 16, 16, 22, 22, 44, 44, 44, 44, 44, 50, 50, 44, 16, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 44, 44, 44, 50, 50, 44, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/316102/xbz-8058115.52/working/building/ZINC001281750435 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281750435 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281750435 Building ZINC001702240208 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702240208 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/868 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702240208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702240208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001702240208 none CC(=O)N1CCC(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 16, 11, 16, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56]) total number of confs: 133 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/869 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702240208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702240208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001702240208 none CC(=O)N1CCC(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 17, 12, 17, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56]) total number of confs: 137 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702240208 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208 Building ZINC001702240208 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702240208 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 868) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(=O)N1CCC(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702240208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702240208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001702240208 none CC(=O)N1CCC(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 16, 11, 16, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56]) total number of confs: 133 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 869) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(=O)N1CCC(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001702240208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702240208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001702240208 none CC(=O)N1CCC(C(=O)N2C[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 17, 12, 17, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56]) total number of confs: 137 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702240208 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702240208 Building ZINC000609871192 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000609871192 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/870 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCc1nnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)s1) `ZINC000609871192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000609871192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000609871192 none COC(=O)CCc1nnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.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.3', 'C.2', 'C.3', '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, 11, 5, 5, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 41, 10, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 41, 41, 41, 25, 25, 10, 10, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/871 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCc1nnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)s1) `ZINC000609871192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000609871192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000609871192 none COC(=O)CCc1nnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.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.3', 'C.2', 'C.3', '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, 11, 5, 5, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 41, 10, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 41, 41, 41, 25, 25, 10, 10, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000609871192 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192 Building ZINC000609871192 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000609871192 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 870) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CCc1nnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)s1) `ZINC000609871192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000609871192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000609871192 none COC(=O)CCc1nnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.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.3', 'C.2', 'C.3', '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, 11, 5, 5, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 41, 10, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 41, 41, 41, 25, 25, 10, 10, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 871) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COC(=O)CCc1nnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)s1) `ZINC000609871192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000609871192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000609871192 none COC(=O)CCc1nnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.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.3', 'C.2', 'C.3', '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, 11, 5, 5, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 41, 10, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 41, 41, 41, 25, 25, 10, 10, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000609871192 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000609871192 Building ZINC001702250961 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702250961 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/872 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C) `ZINC001702250961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702250961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702250961 none CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 23, 23, 23, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/873 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C) `ZINC001702250961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702250961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702250961 none CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 50, 50, 17, 17, 17, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 48, 48, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702250961 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961 Building ZINC001702250961 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702250961 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 872) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C) `ZINC001702250961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702250961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702250961 none CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 23, 23, 23, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 873) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C) `ZINC001702250961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702250961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702250961 none CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 50, 50, 17, 17, 17, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 48, 48, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702250961 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702250961 Building ZINC000558192431 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000558192431 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/874 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000558192431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000558192431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000558192431 none CNS(=O)(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 25, 25, 10, 10, 10, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 10, 10, 31, 31, 31, 31, 10, 10, 10, 10, 10, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/875 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000558192431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000558192431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000558192431 none CNS(=O)(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 23, 7, 23, 23, 7, 7, 7, 5, 2, 5, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 7, 7, 32, 32, 32, 32, 7, 7, 7, 7, 7, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 7, 7, 7, 7] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000558192431 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431 Building ZINC000558192431 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000558192431 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 874) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNS(=O)(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000558192431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000558192431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000558192431 none CNS(=O)(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 25, 25, 10, 10, 10, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 10, 10, 31, 31, 31, 31, 10, 10, 10, 10, 10, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 875) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNS(=O)(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000558192431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000558192431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000558192431 none CNS(=O)(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 23, 7, 23, 23, 7, 7, 7, 5, 2, 5, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 7, 7, 32, 32, 32, 32, 7, 7, 7, 7, 7, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 7, 7, 7, 7] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000558192431 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000558192431 Building ZINC001281785615 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281785615 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/876 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C) `ZINC001281785615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281785615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281785615 none CCCNC(=O)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 36, 24, 36, 24, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 36, 24, 24, 24, 24, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/877 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C) `ZINC001281785615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281785615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281785615 none CCCNC(=O)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 15, 27, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 27, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281785615 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615 Building ZINC001281785615 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281785615 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 876) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCNC(=O)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C) `ZINC001281785615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281785615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281785615 none CCCNC(=O)CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 36, 24, 36, 24, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 36, 24, 24, 24, 24, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 877) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCNC(=O)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C) `ZINC001281785615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281785615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281785615 none CCCNC(=O)CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 15, 27, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 27, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281785615 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281785615 Building ZINC001521541972 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521541972 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/878 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1) `ZINC001521541972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521541972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001521541972 none COC(=O)NCC(=O)N1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 27, 8, 5, 8, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 40, 27, 27, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/879 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1) `ZINC001521541972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521541972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001521541972 none COC(=O)NCC(=O)N1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 26, 8, 5, 8, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 40, 26, 26, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001521541972 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972 Building ZINC001521541972 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521541972 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 878) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1) `ZINC001521541972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521541972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001521541972 none COC(=O)NCC(=O)N1C[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 27, 8, 5, 8, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 40, 27, 27, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 879) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1) `ZINC001521541972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521541972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001521541972 none COC(=O)NCC(=O)N1C[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 26, 8, 5, 8, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 40, 26, 26, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001521541972 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521541972 Building ZINC000243333801 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243333801 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/880 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OC[C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1) `ZINC000243333801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243333801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000243333801 none Cc1ccc(OC[C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 11, 5, 1, 1, 1, 1, 3, 3, 3, 9, 17, 19, 21, 21, 21, 21, 21, 21, 21, 21, 14, 14, 14, 14, 14, 14, 14, 5, 5, 3, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 14, 14] 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: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/881 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OC[C@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1) `ZINC000243333801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243333801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000243333801 none Cc1ccc(OC[C@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 1, 1, 1, 1, 2, 2, 2, 7, 13, 15, 19, 19, 19, 19, 19, 19, 19, 19, 14, 14, 14, 14, 14, 14, 14, 5, 5, 2, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 14, 14] 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: 84 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000243333801 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801 Building ZINC000243333801 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243333801 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 880) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccc(OC[C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1) `ZINC000243333801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243333801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000243333801 none Cc1ccc(OC[C@@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 11, 5, 1, 1, 1, 1, 3, 3, 3, 9, 17, 19, 21, 21, 21, 21, 21, 21, 21, 21, 14, 14, 14, 14, 14, 14, 14, 5, 5, 3, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 14, 14] 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: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 881) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1ccc(OC[C@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1) `ZINC000243333801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243333801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000243333801 none Cc1ccc(OC[C@]([O-])([SiH3])C(=O)NCC(=O)N2CCN(C3CC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 1, 1, 1, 1, 2, 2, 2, 7, 13, 15, 19, 19, 19, 19, 19, 19, 19, 19, 14, 14, 14, 14, 14, 14, 14, 5, 5, 2, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 14, 14] 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: 84 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000243333801 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243333801 Building ZINC001521558643 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521558643 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/882 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCC(N)=O)C[C@@]2(C)C1) `ZINC001521558643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521558643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001521558643 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCC(N)=O)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 6, 6, 6, 6, 6, 8, 8, 25, 25, 46, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 32, 32, 43, 42, 50, 50, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/883 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCC(N)=O)C[C@@]2(C)C1) `ZINC001521558643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521558643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001521558643 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCC(N)=O)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 7, 7, 24, 24, 46, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 24, 24, 32, 32, 42, 42, 50, 50, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001521558643 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643 Building ZINC001521558643 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521558643 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 882) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCC(N)=O)C[C@@]2(C)C1) `ZINC001521558643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521558643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001521558643 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCC(N)=O)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 6, 6, 6, 6, 6, 8, 8, 25, 25, 46, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 32, 32, 43, 42, 50, 50, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 883) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCC(N)=O)C[C@@]2(C)C1) `ZINC001521558643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521558643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001521558643 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCCC(N)=O)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 7, 7, 24, 24, 46, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 24, 24, 32, 32, 42, 42, 50, 50, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001521558643 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521558643 Building ZINC001521559115 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521559115 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/884 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001521559115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521559115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001521559115 none CCC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 24, 9, 6, 9, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 31, 24, 24, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/885 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001521559115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521559115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001521559115 none CCC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 23, 8, 5, 8, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 30, 23, 23, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001521559115 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115 Building ZINC001521559115 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521559115 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 884) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001521559115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521559115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001521559115 none CCC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 24, 9, 6, 9, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 31, 24, 24, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 885) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001521559115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521559115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001521559115 none CCC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 23, 8, 5, 8, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 30, 23, 23, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001521559115 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559115 Building ZINC001521559840 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521559840 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/886 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001521559840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521559840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521559840 none CNC(=O)NCCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 50, 35, 26, 9, 5, 9, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 44, 35, 35, 26, 26, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 198 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/887 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001521559840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521559840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521559840 none CNC(=O)NCCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 34, 25, 9, 5, 9, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 46, 34, 34, 25, 25, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001521559840 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840 Building ZINC001521559840 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521559840 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 886) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)NCCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001521559840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521559840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521559840 none CNC(=O)NCCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 50, 35, 26, 9, 5, 9, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 44, 35, 35, 26, 26, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 198 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 887) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)NCCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001521559840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521559840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521559840 none CNC(=O)NCCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 34, 25, 9, 5, 9, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 46, 34, 34, 25, 25, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 195 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001521559840 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001521559840 Building ZINC001702290405 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702290405 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/888 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)CC(N)=O)C1) `ZINC001702290405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702290405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702290405 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 40, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 12, 40, 40, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/889 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)CC(N)=O)C1) `ZINC001702290405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702290405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702290405 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 7, 7, 6, 7, 7, 4, 4, 4, 11, 11, 11, 44, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 6, 7, 7, 11, 44, 44, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702290405 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405 Building ZINC001702290405 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702290405 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 888) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)CC(N)=O)C1) `ZINC001702290405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702290405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702290405 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 40, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 12, 40, 40, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 889) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)CC(N)=O)C1) `ZINC001702290405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702290405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702290405 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 7, 7, 6, 7, 7, 4, 4, 4, 11, 11, 11, 44, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 6, 7, 7, 11, 44, 44, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702290405 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702290405 Building ZINC001702295319 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702295319 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/890 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COC1CCCC1) `ZINC001702295319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702295319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001702295319 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 18, 45, 50, 50, 50, 50, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/891 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COC1CCCC1) `ZINC001702295319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702295319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001702295319 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 20, 46, 50, 50, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702295319 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319 Building ZINC001702295319 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702295319 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 890) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COC1CCCC1) `ZINC001702295319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702295319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001702295319 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 18, 45, 50, 50, 50, 50, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 891) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COC1CCCC1) `ZINC001702295319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702295319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001702295319 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)COC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 20, 46, 50, 50, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702295319 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702295319 Building ZINC001702297712 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702297712 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/892 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cccn1) `ZINC001702297712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702297712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001702297712 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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: [9, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 31, 41, 50, 50, 50, 50, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 31, 31, 41, 41, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/893 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cccn1) `ZINC001702297712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702297712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001702297712 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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: [13, 8, 8, 8, 8, 5, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 38, 42, 50, 50, 50, 50, 13, 13, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 38, 38, 42, 42, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702297712 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712 Building ZINC001702297712 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702297712 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 892) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cccn1) `ZINC001702297712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702297712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001702297712 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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: [9, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 31, 41, 50, 50, 50, 50, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 31, 31, 41, 41, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 893) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cccn1) `ZINC001702297712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702297712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001702297712 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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: [13, 8, 8, 8, 8, 5, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 38, 42, 50, 50, 50, 50, 13, 13, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 38, 38, 42, 42, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702297712 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702297712 Building ZINC001702301733 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301733 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/894 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)COc2cccnc2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702301733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001702301733 none CO[C@@H]1CN(C(=O)COc2cccnc2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 7, 7, 9, 9, 22, 37, 50, 50, 50, 50, 50, 7, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 22, 22, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/895 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)COc2cccnc2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702301733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001702301733 none CO[C@@H]1CN(C(=O)COc2cccnc2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 8, 8, 22, 37, 50, 50, 50, 50, 50, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 6, 6, 22, 22, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301733 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733 Building ZINC001702301733 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301733 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 894) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)COc2cccnc2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702301733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001702301733 none CO[C@@H]1CN(C(=O)COc2cccnc2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 7, 7, 9, 9, 22, 37, 50, 50, 50, 50, 50, 7, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 22, 22, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 895) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)COc2cccnc2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702301733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001702301733 none CO[C@@H]1CN(C(=O)COc2cccnc2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 8, 8, 22, 37, 50, 50, 50, 50, 50, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 6, 6, 22, 22, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301733 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301733 Building ZINC001702301259 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301259 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/896 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CCc2nccn2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702301259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001702301259 none CO[C@@H]1CN(C(=O)CCc2nccn2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 25, 27, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 8, 8, 25, 25, 27, 27, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/897 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CCc2nccn2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702301259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001702301259 none CO[C@@H]1CN(C(=O)CCc2nccn2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 13, 13, 23, 24, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 8, 8, 23, 23, 24, 24, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301259 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259 Building ZINC001702301259 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301259 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 896) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)CCc2nccn2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702301259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001702301259 none CO[C@@H]1CN(C(=O)CCc2nccn2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 25, 27, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 8, 8, 25, 25, 27, 27, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 897) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)CCc2nccn2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702301259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001702301259 none CO[C@@H]1CN(C(=O)CCc2nccn2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 13, 13, 23, 24, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 8, 8, 23, 23, 24, 24, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301259 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301259 Building ZINC001702301449 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301449 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/898 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cnc(C)nc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702301449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702301449 none CO[C@@H]1CN(C(=O)c2cnc(C)nc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 5, 8, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 14, 14, 14, 14, 14, 14, 31, 31, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/899 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cnc(C)nc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702301449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702301449 none CO[C@@H]1CN(C(=O)c2cnc(C)nc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 5, 8, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 12, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301449 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449 Building ZINC001702301449 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301449 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 898) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2cnc(C)nc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702301449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702301449 none CO[C@@H]1CN(C(=O)c2cnc(C)nc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 5, 8, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 14, 14, 14, 14, 14, 14, 31, 31, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 899) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2cnc(C)nc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702301449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702301449 none CO[C@@H]1CN(C(=O)c2cnc(C)nc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 5, 8, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 12, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301449 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301449 Building ZINC001702301457 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301457 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/900 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1) `ZINC001702301457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001702301457 none COc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.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, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 12, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need 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, 27, 16, 27, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 23, 16, 45, 45, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 16, 16, 45] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 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/316102/xbz-8058115.52/working/building/ZINC001702301457 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/901 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1) `ZINC001702301457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001702301457 none COc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.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, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 12, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need 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, 27, 15, 27, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 20, 15, 48, 48, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 15, 15, 48] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301457 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457 Building ZINC001702301457 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301457 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 900) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1) `ZINC001702301457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001702301457 none COc1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.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, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 12, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need 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, 27, 16, 27, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 23, 16, 45, 45, 50, 50, 50, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 16, 16, 45] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 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/316102/xbz-8058115.52/working/building/ZINC001702301457 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 901) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1) `ZINC001702301457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001702301457 none COc1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.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, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 12, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need 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, 27, 15, 27, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 20, 15, 48, 48, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 15, 15, 48] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301457 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301457 Building ZINC001702302300 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702302300 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/902 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccnc(F)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702302300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702302300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001702302300 none CO[C@@H]1CN(C(=O)c2ccnc(F)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 23, 23, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/903 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccnc(F)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702302300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702302300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001702302300 none CO[C@@H]1CN(C(=O)c2ccnc(F)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 12, 12, 12, 24, 24, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 12, 12, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702302300 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300 Building ZINC001702302300 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702302300 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 902) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2ccnc(F)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702302300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702302300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001702302300 none CO[C@@H]1CN(C(=O)c2ccnc(F)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 23, 23, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 903) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2ccnc(F)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702302300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702302300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001702302300 none CO[C@@H]1CN(C(=O)c2ccnc(F)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 12, 12, 12, 24, 24, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 12, 12, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702302300 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302300 Building ZINC001702301768 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301768 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/904 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CCc2nc(C)no2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702301768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702301768 none CO[C@@H]1CN(C(=O)CCc2nc(C)no2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 5, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 11, 11, 16, 18, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 18, 18, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/905 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CCc2nc(C)no2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702301768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702301768 none CO[C@@H]1CN(C(=O)CCc2nc(C)no2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 5, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 8, 8, 13, 13, 19, 21, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 8, 8, 19, 19, 21, 21, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301768 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768 Building ZINC001702301768 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301768 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 904) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)CCc2nc(C)no2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702301768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702301768 none CO[C@@H]1CN(C(=O)CCc2nc(C)no2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 5, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 11, 11, 16, 18, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 18, 18, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 905) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)CCc2nc(C)no2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702301768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001702301768 none CO[C@@H]1CN(C(=O)CCc2nc(C)no2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 5, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 8, 8, 13, 13, 19, 21, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 8, 8, 19, 19, 21, 21, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301768 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301768 Building ZINC001702301832 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301832 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/906 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001702301832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702301832 none CCn1ccnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 30, 16, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 9, 50, 50, 50, 50, 50, 30, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 9, 9] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/907 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001702301832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702301832 none CCn1ccnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 32, 19, 11, 19, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 15, 11, 50, 50, 50, 50, 50, 32, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301832 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832 Building ZINC001702301832 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301832 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 906) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCn1ccnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001702301832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702301832 none CCn1ccnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 30, 16, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 9, 50, 50, 50, 50, 50, 30, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 9, 9] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 907) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCn1ccnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001702301832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702301832 none CCn1ccnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 32, 19, 11, 19, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 15, 11, 50, 50, 50, 50, 50, 32, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301832 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301832 Building ZINC001702301847 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301847 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/908 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001702301847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702301847 none COCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 32, 32, 14, 6, 14, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 32, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/909 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001702301847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702301847 none COCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 30, 30, 30, 30, 30, 11, 7, 11, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 7, 50, 50, 50, 48, 48, 30, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301847 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847 Building ZINC001702301847 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702301847 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 908) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001702301847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702301847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702301847 none COCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 32, 32, 14, 6, 14, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 32, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 909) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001702301847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702301847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702301847 none COCc1nocc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 30, 30, 30, 30, 30, 11, 7, 11, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 7, 50, 50, 50, 48, 48, 30, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702301847 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702301847 Building ZINC001702302106 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702302106 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/910 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)Cc2[nH]cnc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702302106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702302106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001702302106 none CO[C@@H]1CN(C(=O)Cc2[nH]cnc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 8, 6, 1, 8, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 8, 8, 8, 8, 8, 14, 14, 40, 50, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 8, 8, 40, 40, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/911 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)Cc2[nH]cnc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702302106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702302106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001702302106 none CO[C@@H]1CN(C(=O)Cc2[nH]cnc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 8, 6, 1, 8, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 14, 14, 42, 50, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 8, 8, 42, 42, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702302106 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106 Building ZINC001702302106 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702302106 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 910) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)Cc2[nH]cnc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702302106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702302106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001702302106 none CO[C@@H]1CN(C(=O)Cc2[nH]cnc2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 8, 6, 1, 8, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 8, 8, 8, 8, 8, 14, 14, 40, 50, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 8, 8, 40, 40, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 911) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)Cc2[nH]cnc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702302106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702302106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001702302106 none CO[C@@H]1CN(C(=O)Cc2[nH]cnc2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 8, 6, 1, 8, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 14, 14, 42, 50, 50, 50, 50, 50, 50, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 8, 8, 42, 42, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702302106 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302106 Building ZINC001702302567 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702302567 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/912 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C23CCN(CC2)C3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702302567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702302567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001702302567 none CO[C@@H]1CN(C(=O)C23CCN(CC2)C3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 15, 15, 15, 15, 15, 43, 43, 50, 50, 50, 50, 50, 50, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 146 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/913 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C23CCN(CC2)C3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702302567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702302567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001702302567 none CO[C@@H]1CN(C(=O)C23CCN(CC2)C3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 41, 41, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702302567 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567 Building ZINC001702302567 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702302567 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 912) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)C23CCN(CC2)C3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001702302567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702302567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001702302567 none CO[C@@H]1CN(C(=O)C23CCN(CC2)C3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 15, 15, 15, 15, 15, 43, 43, 50, 50, 50, 50, 50, 50, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 146 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 913) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)C23CCN(CC2)C3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001702302567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702302567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001702302567 none CO[C@@H]1CN(C(=O)C23CCN(CC2)C3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 41, 41, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702302567 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702302567 Building ZINC000390208072 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000390208072 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/914 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(O)[C@]([O-])([SiH3])C(=O)NCCc1ccc(I)s1) `ZINC000390208072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000390208072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 27 natoms 26 natoms 25 natoms 24 names: ZINC000390208072 none O=C(O)[C@]([O-])([SiH3])C(=O)NCCc1ccc(I)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'I', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 18, 14, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 9, 4, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 4, 4, 4, 17, 27, 41, 41, 41, 41, 41, 15, 4, 17, 17, 27, 27, 41, 41] 150 rigid atoms, others: [1, 3, 4, 5] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/915 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(O)[C@@]([O-])([SiH3])C(=O)NCCc1ccc(I)s1) `ZINC000390208072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000390208072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 27 natoms 26 natoms 25 natoms 24 names: ZINC000390208072 none O=C(O)[C@@]([O-])([SiH3])C(=O)NCCc1ccc(I)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'I', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 18, 14, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 9, 4, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 4, 4, 4, 16, 27, 41, 41, 41, 41, 41, 18, 4, 16, 16, 27, 27, 41, 41] 150 rigid atoms, others: [1, 3, 4, 5] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000390208072 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072 Building ZINC000390208072 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000390208072 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 914) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(O)[C@]([O-])([SiH3])C(=O)NCCc1ccc(I)s1) `ZINC000390208072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000390208072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 27 natoms 26 natoms 25 natoms 24 names: ZINC000390208072 none O=C(O)[C@]([O-])([SiH3])C(=O)NCCc1ccc(I)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'I', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 18, 14, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 9, 4, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 4, 4, 4, 17, 27, 41, 41, 41, 41, 41, 15, 4, 17, 17, 27, 27, 41, 41] 150 rigid atoms, others: [1, 3, 4, 5] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 915) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(O)[C@@]([O-])([SiH3])C(=O)NCCc1ccc(I)s1) `ZINC000390208072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000390208072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 27 natoms 26 natoms 25 natoms 24 names: ZINC000390208072 none O=C(O)[C@@]([O-])([SiH3])C(=O)NCCc1ccc(I)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'I', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 18, 14, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 9, 4, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 4, 4, 4, 16, 27, 41, 41, 41, 41, 41, 18, 4, 16, 16, 27, 27, 41, 41] 150 rigid atoms, others: [1, 3, 4, 5] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000390208072 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000390208072 Building ZINC000584812880 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584812880 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/916 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCn1cc(CO)nn1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000584812880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584812880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000584812880 none O=C(NCCCn1cc(CO)nn1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 12, 8, 8, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 16, 16, 31, 49, 49, 49, 50, 49, 49, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 16, 16, 24, 24, 28, 27, 49, 50, 50, 150, 2, 2, 2, 2] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/917 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCn1cc(CO)nn1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000584812880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584812880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000584812880 none O=C(NCCCn1cc(CO)nn1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 12, 8, 8, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 16, 15, 31, 49, 49, 48, 50, 49, 49, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 16, 16, 24, 24, 28, 27, 49, 50, 50, 150, 2, 2, 2, 2] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000584812880 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880 Building ZINC000584812880 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000584812880 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 916) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCCn1cc(CO)nn1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000584812880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000584812880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000584812880 none O=C(NCCCn1cc(CO)nn1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 12, 8, 8, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 16, 16, 31, 49, 49, 49, 50, 49, 49, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 16, 16, 24, 24, 28, 27, 49, 50, 50, 150, 2, 2, 2, 2] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 917) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(NCCCn1cc(CO)nn1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000584812880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000584812880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000584812880 none O=C(NCCCn1cc(CO)nn1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 12, 8, 8, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 16, 15, 31, 49, 49, 48, 50, 49, 49, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 16, 16, 24, 24, 28, 27, 49, 50, 50, 150, 2, 2, 2, 2] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000584812880 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000584812880 Building ZINC001343820213 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343820213 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/918 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)CC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001343820213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343820213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343820213 none CCS(=O)(=O)CC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 50, 23, 15, 23, 15, 15, 15, 15, 15, 15, 13, 2, 13, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 37, 37, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/919 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)CC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001343820213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343820213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343820213 none CCS(=O)(=O)CC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 50, 50, 21, 14, 21, 14, 14, 14, 14, 14, 14, 12, 2, 12, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 38, 38, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 206 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343820213 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213 Building ZINC001343820213 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343820213 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 918) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCS(=O)(=O)CC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001343820213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343820213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343820213 none CCS(=O)(=O)CC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 50, 23, 15, 23, 15, 15, 15, 15, 15, 15, 13, 2, 13, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 37, 37, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 919) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCS(=O)(=O)CC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001343820213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343820213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343820213 none CCS(=O)(=O)CC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 50, 50, 21, 14, 21, 14, 14, 14, 14, 14, 14, 12, 2, 12, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 38, 38, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 206 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343820213 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820213 Building ZINC001343820320 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343820320 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/920 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1)C(=O)C1CC1) `ZINC001343820320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343820320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001343820320 none CN(CC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 16, 15, 16, 15, 15, 15, 15, 15, 15, 11, 1, 11, 1, 1, 1, 1, 1, 1, 15, 15, 15, 30, 38, 38, 50, 50, 30, 30, 30, 23, 23, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/921 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1)C(=O)C1CC1) `ZINC001343820320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343820320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001343820320 none CN(CC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 22, 18, 22, 18, 18, 18, 18, 18, 18, 13, 1, 13, 1, 1, 1, 1, 1, 1, 18, 18, 18, 34, 41, 41, 50, 50, 34, 34, 34, 25, 25, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343820320 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320 Building ZINC001343820320 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343820320 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 920) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(CC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1)C(=O)C1CC1) `ZINC001343820320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343820320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001343820320 none CN(CC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 16, 15, 16, 15, 15, 15, 15, 15, 15, 11, 1, 11, 1, 1, 1, 1, 1, 1, 15, 15, 15, 30, 38, 38, 50, 50, 30, 30, 30, 23, 23, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 921) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(CC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1)C(=O)C1CC1) `ZINC001343820320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343820320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001343820320 none CN(CC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 22, 18, 22, 18, 18, 18, 18, 18, 18, 13, 1, 13, 1, 1, 1, 1, 1, 1, 18, 18, 18, 34, 41, 41, 50, 50, 34, 34, 34, 25, 25, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343820320 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343820320 Building ZINC001343821425 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343821425 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/922 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001343821425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343821425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001343821425 none CNC(=O)CCCCC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 21, 18, 19, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 36, 36, 21, 21, 21, 21, 19, 19, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/923 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001343821425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343821425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001343821425 none CNC(=O)CCCCC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 50, 19, 18, 16, 13, 12, 13, 12, 12, 12, 12, 12, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 33, 33, 19, 19, 18, 18, 16, 16, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343821425 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425 Building ZINC001343821425 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343821425 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 922) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)CCCCC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001343821425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343821425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001343821425 none CNC(=O)CCCCC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 21, 18, 19, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 36, 36, 21, 21, 21, 21, 19, 19, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 923) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)CCCCC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001343821425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343821425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001343821425 none CNC(=O)CCCCC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 50, 19, 18, 16, 13, 12, 13, 12, 12, 12, 12, 12, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 33, 33, 19, 19, 18, 18, 16, 16, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343821425 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821425 Building ZINC001281823548 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281823548 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/924 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ocnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001281823548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281823548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001281823548 none CCc1ocnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 42, 42, 42, 18, 9, 18, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 9, 50, 50, 50, 50, 50, 42, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 9, 9] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/925 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ocnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001281823548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281823548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001281823548 none CCc1ocnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 44, 44, 44, 44, 18, 11, 18, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 15, 11, 50, 50, 50, 50, 50, 44, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 11, 11] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281823548 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548 Building ZINC001281823548 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281823548 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 924) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCc1ocnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001281823548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281823548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001281823548 none CCc1ocnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 42, 42, 42, 18, 9, 18, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 9, 50, 50, 50, 50, 50, 42, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 9, 9] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 925) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCc1ocnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001281823548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281823548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001281823548 none CCc1ocnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 1, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 44, 44, 44, 44, 18, 11, 18, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 15, 11, 50, 50, 50, 50, 50, 44, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 11, 11] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281823548 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823548 Building ZINC001343821813 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343821813 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/926 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@@H]3CCOC3)C[C@H]21) `ZINC001343821813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343821813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001343821813 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 32, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 11, 11, 31, 31, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/927 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@@H]3CCOC3)C[C@H]21) `ZINC001343821813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343821813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001343821813 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 9, 18, 39, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 38, 38, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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/316102/xbz-8058115.52/working/building/ZINC001343821813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343821813 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813 Building ZINC001343821813 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343821813 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 926) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@@H]3CCOC3)C[C@H]21) `ZINC001343821813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343821813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001343821813 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 32, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 11, 11, 31, 31, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 927) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@@H]3CCOC3)C[C@H]21) `ZINC001343821813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343821813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001343821813 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 9, 18, 39, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 38, 38, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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/316102/xbz-8058115.52/working/building/ZINC001343821813 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343821813 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821813 Building ZINC001343821814 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343821814 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/928 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@H]3CCOC3)C[C@H]21) `ZINC001343821814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343821814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001343821814 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 23, 35, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 33, 33, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/929 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@H]3CCOC3)C[C@H]21) `ZINC001343821814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343821814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001343821814 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 10, 18, 37, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 10, 10, 37, 37, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343821814 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814 Building ZINC001343821814 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343821814 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 928) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@H]3CCOC3)C[C@H]21) `ZINC001343821814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343821814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001343821814 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 23, 35, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 33, 33, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 929) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@H]3CCOC3)C[C@H]21) `ZINC001343821814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343821814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001343821814 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(C(=O)COC[C@H]3CCOC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 10, 18, 37, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 10, 10, 37, 37, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001343821814 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001343821814 Building ZINC001281823658 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281823658 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/930 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)on1) `ZINC001281823658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281823658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001281823658 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 26, 13, 26, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 20, 13, 48, 48, 50, 50, 50, 48, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 13, 13] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/931 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)on1) `ZINC001281823658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281823658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001281823658 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 17, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 12, 12] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281823658 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658 Building ZINC001281823658 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281823658 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 930) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)on1) `ZINC001281823658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281823658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001281823658 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 26, 13, 26, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 20, 13, 48, 48, 50, 50, 50, 48, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 13, 13] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 931) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)on1) `ZINC001281823658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281823658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001281823658 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 17, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 12, 12] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281823658 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281823658 Building ZINC001281824023 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281824023 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/932 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cc(C)nn2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281824023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281824023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001281824023 none CO[C@@H]1CN(C(=O)c2cc(C)nn2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 5, 8, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 13, 13, 13, 13, 13, 29, 29, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/933 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cc(C)nn2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281824023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281824023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001281824023 none CO[C@@H]1CN(C(=O)c2cc(C)nn2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 5, 8, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/316102/xbz-8058115.52/working/building/ZINC001281824023 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281824023 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023 Building ZINC001281824023 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281824023 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 932) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2cc(C)nn2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281824023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281824023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001281824023 none CO[C@@H]1CN(C(=O)c2cc(C)nn2C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 5, 8, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 13, 13, 13, 13, 13, 29, 29, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 933) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2cc(C)nn2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281824023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281824023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001281824023 none CO[C@@H]1CN(C(=O)c2cc(C)nn2C)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 5, 8, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/316102/xbz-8058115.52/working/building/ZINC001281824023 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281824023 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824023 Building ZINC001702310094 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702310094 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/934 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1) `ZINC001702310094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702310094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001702310094 none COCCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 28, 10, 10, 10, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 28, 28, 50, 50, 50, 50, 50, 32, 32, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 28, 28, 28, 28] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/935 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1) `ZINC001702310094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702310094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001702310094 none COCCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 27, 8, 8, 8, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 27, 27, 50, 50, 50, 50, 50, 33, 33, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 27, 27, 27, 27] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702310094 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094 Building ZINC001702310094 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702310094 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 934) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1) `ZINC001702310094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702310094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001702310094 none COCCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 28, 10, 10, 10, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 28, 28, 50, 50, 50, 50, 50, 32, 32, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 28, 28, 28, 28] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 935) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1) `ZINC001702310094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702310094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001702310094 none COCCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 27, 8, 8, 8, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 27, 27, 50, 50, 50, 50, 50, 33, 33, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 27, 27, 27, 27] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702310094 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702310094 Building ZINC001702313675 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702313675 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/936 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cnc[nH]1) `ZINC001702313675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702313675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001702313675 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 12, 38, 47, 50, 50, 50, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 38, 38, 47, 47, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/937 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cnc[nH]1) `ZINC001702313675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702313675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001702313675 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 18, 18, 18, 42, 49, 50, 50, 50, 50, 50, 14, 14, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 18, 42, 42, 49, 49, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702313675 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675 Building ZINC001702313675 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702313675 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 936) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cnc[nH]1) `ZINC001702313675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702313675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001702313675 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 12, 38, 47, 50, 50, 50, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 38, 38, 47, 47, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 937) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cnc[nH]1) `ZINC001702313675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702313675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001702313675 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 18, 18, 18, 42, 49, 50, 50, 50, 50, 50, 14, 14, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 18, 42, 42, 49, 49, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702313675 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702313675 Building ZINC001702314573 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702314573 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/938 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 25, 44, 50, 50, 50, 50, 50, 50, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 25, 25, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/939 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 37, 49, 50, 50, 50, 50, 50, 50, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 37, 37, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/940 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/940' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 25, 44, 50, 50, 50, 50, 50, 50, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 25, 25, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/941 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/941' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 37, 49, 50, 50, 50, 50, 50, 50, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 37, 37, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702314573 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 Building ZINC001702314573 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702314573 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 938) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 25, 44, 50, 50, 50, 50, 50, 50, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 25, 25, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 939) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 37, 49, 50, 50, 50, 50, 50, 50, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 37, 37, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 940) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 25, 44, 50, 50, 50, 50, 50, 50, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 25, 25, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 941) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 37, 49, 50, 50, 50, 50, 50, 50, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 37, 37, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702314573 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 Building ZINC001702314573 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702314573 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 938) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 25, 44, 50, 50, 50, 50, 50, 50, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 25, 25, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 939) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 37, 49, 50, 50, 50, 50, 50, 50, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 37, 37, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 940) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 25, 44, 50, 50, 50, 50, 50, 50, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 25, 25, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 941) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 37, 49, 50, 50, 50, 50, 50, 50, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 37, 37, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702314573 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 Building ZINC001702314573 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702314573 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 938) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 25, 44, 50, 50, 50, 50, 50, 50, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 25, 25, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 939) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 37, 49, 50, 50, 50, 50, 50, 50, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 37, 37, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 940) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 25, 44, 50, 50, 50, 50, 50, 50, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 25, 25, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 941) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C) `ZINC001702314573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702314573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314573 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 37, 49, 50, 50, 50, 50, 50, 50, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 37, 37, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702314573 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314573 Building ZINC001702314574 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702314574 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/942 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 33, 46, 50, 50, 50, 50, 50, 50, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 33, 33, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/943 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 38, 47, 50, 50, 50, 50, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 38, 38, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/944 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/944' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 33, 46, 50, 50, 50, 50, 50, 50, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 33, 33, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/945 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/945' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 38, 47, 50, 50, 50, 50, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 38, 38, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702314574 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 Building ZINC001702314574 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702314574 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 942) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 33, 46, 50, 50, 50, 50, 50, 50, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 33, 33, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 943) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 38, 47, 50, 50, 50, 50, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 38, 38, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 944) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 33, 46, 50, 50, 50, 50, 50, 50, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 33, 33, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 945) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 38, 47, 50, 50, 50, 50, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 38, 38, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702314574 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 Building ZINC001702314574 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702314574 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 942) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 33, 46, 50, 50, 50, 50, 50, 50, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 33, 33, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 943) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 38, 47, 50, 50, 50, 50, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 38, 38, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 944) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 33, 46, 50, 50, 50, 50, 50, 50, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 33, 33, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 945) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 38, 47, 50, 50, 50, 50, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 38, 38, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702314574 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 Building ZINC001702314574 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001702314574 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 942) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 33, 46, 50, 50, 50, 50, 50, 50, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 33, 33, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 943) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 38, 47, 50, 50, 50, 50, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 38, 38, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `2' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/2 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 2 (index: 944) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 33, 46, 50, 50, 50, 50, 50, 50, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 33, 33, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `3' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/3 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 3 (index: 945) grep: /scratch/xiaobo/316102/xbz-8058115.52/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C) `ZINC001702314574.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001702314574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001702314574 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CC[C@@H]1CCCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 38, 47, 50, 50, 50, 50, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 38, 38, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702314574 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 2: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/2.* 3: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/3.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702314574 Building ZINC000243380293 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243380293 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/946 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])Cc1ccc(Cl)cc1)N1CCN(C2CC2)CC1) `ZINC000243380293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243380293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000243380293 none O=C(CNC(=O)[C@]([O-])([SiH3])Cc1ccc(Cl)cc1)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 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: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 42, 49, 49, 49, 49, 49, 49, 49, 49, 11, 11, 3, 4, 4, 4, 4, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/947 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])Cc1ccc(Cl)cc1)N1CCN(C2CC2)CC1) `ZINC000243380293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243380293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000243380293 none O=C(CNC(=O)[C@@]([O-])([SiH3])Cc1ccc(Cl)cc1)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 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: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 46, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 131 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000243380293 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293 Building ZINC000243380293 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243380293 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 946) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@]([O-])([SiH3])Cc1ccc(Cl)cc1)N1CCN(C2CC2)CC1) `ZINC000243380293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243380293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000243380293 none O=C(CNC(=O)[C@]([O-])([SiH3])Cc1ccc(Cl)cc1)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 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: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 42, 49, 49, 49, 49, 49, 49, 49, 49, 11, 11, 3, 4, 4, 4, 4, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 947) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@@]([O-])([SiH3])Cc1ccc(Cl)cc1)N1CCN(C2CC2)CC1) `ZINC000243380293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243380293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000243380293 none O=C(CNC(=O)[C@@]([O-])([SiH3])Cc1ccc(Cl)cc1)N1CCN(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 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: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 46, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 131 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000243380293 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000243380293 Building ZINC001281824213 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281824213 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/948 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2F)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281824213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281824213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281824213 none CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2F)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 5, 8, 8, 5, 1, 15, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/949 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2F)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281824213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281824213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281824213 none CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2F)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 5, 8, 8, 5, 1, 15, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 24, 24, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/316102/xbz-8058115.52/working/building/ZINC001281824213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281824213 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213 Building ZINC001281824213 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281824213 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 948) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2F)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281824213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281824213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281824213 none CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2F)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 5, 8, 8, 5, 1, 15, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 949) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2F)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281824213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281824213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001281824213 none CO[C@@H]1CN(C(=O)c2c(C)nn(C)c2F)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 5, 8, 8, 5, 1, 15, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 24, 24, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/316102/xbz-8058115.52/working/building/ZINC001281824213 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281824213 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824213 Building ZINC001281824589 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281824589 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/950 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cc(C)nc(C)n2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281824589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281824589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001281824589 none CO[C@@H]1CN(C(=O)c2cc(C)nc(C)n2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 5, 8, 1, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 21, 21, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/316102/xbz-8058115.52/working/building/ZINC001281824589 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/951 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cc(C)nc(C)n2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281824589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281824589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001281824589 none CO[C@@H]1CN(C(=O)c2cc(C)nc(C)n2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 5, 8, 1, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 11, 11, 11, 11, 11, 20, 20, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281824589 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589 Building ZINC001281824589 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281824589 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 950) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2cc(C)nc(C)n2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281824589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281824589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001281824589 none CO[C@@H]1CN(C(=O)c2cc(C)nc(C)n2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 5, 8, 1, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 21, 21, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/316102/xbz-8058115.52/working/building/ZINC001281824589 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 951) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2cc(C)nc(C)n2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281824589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281824589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001281824589 none CO[C@@H]1CN(C(=O)c2cc(C)nc(C)n2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 5, 8, 1, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 11, 11, 11, 11, 11, 20, 20, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281824589 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824589 Building ZINC001281824597 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281824597 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/952 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cncc(F)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281824597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281824597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001281824597 none CO[C@@H]1CN(C(=O)c2cncc(F)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 12, 12, 12, 24, 24, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 12, 12, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/953 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cncc(F)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281824597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281824597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001281824597 none CO[C@@H]1CN(C(=O)c2cncc(F)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 12, 12, 12, 25, 25, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 12, 12, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281824597 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597 Building ZINC001281824597 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281824597 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 952) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2cncc(F)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281824597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281824597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001281824597 none CO[C@@H]1CN(C(=O)c2cncc(F)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 12, 12, 12, 24, 24, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 12, 12, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 953) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2cncc(F)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281824597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281824597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001281824597 none CO[C@@H]1CN(C(=O)c2cncc(F)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 12, 12, 12, 25, 25, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 12, 12, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281824597 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824597 Building ZINC001281824599 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281824599 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/954 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C) `ZINC001281824599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281824599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001281824599 none CCc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 8, 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, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 21, 10, 21, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 14, 10, 36, 36, 36, 36, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10, 36, 36, 36, 36] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/955 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C) `ZINC001281824599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281824599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001281824599 none CCc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 8, 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, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 21, 10, 21, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 13, 10, 37, 37, 37, 37, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 10, 10, 37, 37, 37, 37] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281824599 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599 Building ZINC001281824599 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281824599 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 954) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C) `ZINC001281824599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281824599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001281824599 none CCc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 8, 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, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 21, 10, 21, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 14, 10, 36, 36, 36, 36, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10, 36, 36, 36, 36] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 955) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C) `ZINC001281824599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281824599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001281824599 none CCc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 8, 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, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 21, 10, 21, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 13, 10, 37, 37, 37, 37, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 10, 10, 37, 37, 37, 37] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281824599 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824599 Building ZINC001281824474 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281824474 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/956 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cnn3c2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281824474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281824474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001281824474 none CO[C@@H]1CN(C(=O)c2cnn3c2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/957 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cnn3c2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281824474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281824474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001281824474 none CO[C@@H]1CN(C(=O)c2cnn3c2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281824474 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474 Building ZINC001281824474 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281824474 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 956) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2cnn3c2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001281824474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281824474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001281824474 none CO[C@@H]1CN(C(=O)c2cnn3c2CCC3)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 957) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)c2cnn3c2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001281824474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281824474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001281824474 none CO[C@@H]1CN(C(=O)c2cnn3c2CCC3)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281824474 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281824474 Building ZINC001281825442 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281825442 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/958 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001281825442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281825442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281825442 none CCCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 35, 11, 35, 11, 6, 4, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 35, 11, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4] 50 rigid atoms, others: [48, 50, 51, 49, 44, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/959 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001281825442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281825442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281825442 none CCCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 32, 32, 10, 32, 10, 8, 5, 8, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 5, 50, 50, 50, 50, 50, 49, 49, 32, 10, 10, 10, 10, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 5] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281825442 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442 Building ZINC001281825442 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281825442 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 958) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001281825442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281825442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281825442 none CCCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 35, 11, 35, 11, 6, 4, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 35, 11, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4] 50 rigid atoms, others: [48, 50, 51, 49, 44, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53, 54, 55, 56]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 959) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001281825442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281825442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281825442 none CCCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 32, 32, 10, 32, 10, 8, 5, 8, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 5, 50, 50, 50, 50, 50, 49, 49, 32, 10, 10, 10, 10, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 5] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281825442 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281825442 Building ZINC001702319839 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702319839 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/960 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C(C)C)N(C)C) `ZINC001702319839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702319839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001702319839 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C(C)C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 19, 19, 19, 6, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 41, 41, 41, 50, 50, 50, 48, 50, 50, 50, 27, 27, 27, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 180 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/961 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C(C)C)N(C)C) `ZINC001702319839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702319839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001702319839 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C(C)C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 6, 1, 7, 1, 1, 1, 2, 2, 2, 16, 16, 16, 16, 34, 34, 34, 49, 49, 50, 46, 49, 50, 50, 25, 25, 25, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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: 225 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702319839 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839 Building ZINC001702319839 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702319839 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 960) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C(C)C)N(C)C) `ZINC001702319839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702319839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001702319839 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C(C)C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 19, 19, 19, 6, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 41, 41, 41, 50, 50, 50, 48, 50, 50, 50, 27, 27, 27, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 180 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 961) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C(C)C)N(C)C) `ZINC001702319839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702319839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001702319839 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C(C)C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 6, 1, 7, 1, 1, 1, 2, 2, 2, 16, 16, 16, 16, 34, 34, 34, 49, 49, 50, 46, 49, 50, 50, 25, 25, 25, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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: 225 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702319839 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702319839 Building ZINC001281826106 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281826106 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/962 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001281826106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281826106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281826106 none CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 50, 26, 23, 22, 7, 5, 7, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 5, 50, 50, 50, 50, 39, 39, 25, 26, 26, 26, 22, 22, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 5, 5] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/963 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001281826106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281826106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281826106 none CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 50, 28, 25, 23, 9, 7, 9, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 8, 7, 50, 50, 50, 50, 39, 39, 28, 28, 28, 28, 23, 23, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281826106 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106 Building ZINC001281826106 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281826106 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 962) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001281826106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281826106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281826106 none CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 50, 26, 23, 22, 7, 5, 7, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 5, 50, 50, 50, 50, 39, 39, 25, 26, 26, 26, 22, 22, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 5, 5] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 963) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001281826106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281826106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001281826106 none CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 50, 28, 25, 23, 9, 7, 9, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 8, 7, 50, 50, 50, 50, 39, 39, 28, 28, 28, 28, 23, 23, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281826106 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281826106 Building ZINC001281832597 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281832597 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/964 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CNC(=O)C(C)(C)C) `ZINC001281832597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281832597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001281832597 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CNC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 24, 24, 24, 38, 50, 50, 50, 50, 50, 50, 16, 16, 16, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 24, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/965 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CNC(=O)C(C)(C)C) `ZINC001281832597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281832597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001281832597 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CNC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 17, 17, 29, 50, 50, 50, 50, 50, 50, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281832597 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597 Building ZINC001281832597 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281832597 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 964) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CNC(=O)C(C)(C)C) `ZINC001281832597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281832597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001281832597 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CNC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 24, 24, 24, 38, 50, 50, 50, 50, 50, 50, 16, 16, 16, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 24, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 965) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CNC(=O)C(C)(C)C) `ZINC001281832597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281832597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001281832597 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CNC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 17, 17, 29, 50, 50, 50, 50, 50, 50, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281832597 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281832597 Building ZINC000514673901 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000514673901 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/966 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)N1CCNCC1) `ZINC000514673901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000514673901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000514673901 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)N1CCNCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 5, 5, 10, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 41, 48, 48, 48, 48, 48, 16, 16, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48] 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]) total number of confs: 146 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/967 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)N1CCNCC1) `ZINC000514673901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000514673901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000514673901 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)N1CCNCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 5, 5, 10, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 43, 48, 48, 48, 48, 48, 14, 14, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48] 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]) total number of confs: 147 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000514673901 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901 Building ZINC000514673901 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000514673901 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 966) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)N1CCNCC1) `ZINC000514673901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000514673901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000514673901 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)N1CCNCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 5, 5, 10, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 41, 48, 48, 48, 48, 48, 16, 16, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48] 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]) total number of confs: 146 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 967) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)N1CCNCC1) `ZINC000514673901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000514673901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000514673901 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)N1CCNCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 5, 5, 10, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 43, 48, 48, 48, 48, 48, 14, 14, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48] 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]) total number of confs: 147 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC000514673901 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC000514673901 Building ZINC001281836349 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281836349 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/968 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccncn1) `ZINC001281836349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281836349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001281836349 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need 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, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 31, 39, 50, 50, 50, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 31, 31, 39, 39, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/969 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccncn1) `ZINC001281836349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281836349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001281836349 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 41, 44, 50, 50, 50, 50, 50, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 41, 41, 44, 44, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281836349 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349 Building ZINC001281836349 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281836349 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 968) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccncn1) `ZINC001281836349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281836349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001281836349 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need 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, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 31, 39, 50, 50, 50, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 31, 31, 39, 39, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 969) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccncn1) `ZINC001281836349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281836349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001281836349 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 41, 44, 50, 50, 50, 50, 50, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 41, 41, 44, 44, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281836349 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281836349 Building ZINC001281839339 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281839339 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/970 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C1(N(C)C)CCC1) `ZINC001281839339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281839339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281839339 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C1(N(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 14, 14, 14, 3, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 32, 32, 50, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 159 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/971 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C1(N(C)C)CCC1) `ZINC001281839339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281839339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281839339 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C1(N(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 12, 12, 12, 5, 1, 6, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 28, 28, 28, 48, 49, 49, 48, 48, 48, 20, 20, 20, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 28, 49, 49, 49, 49, 49, 49, 48, 48, 48, 48, 48, 48] 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]) total number of confs: 172 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281839339 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339 Building ZINC001281839339 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001281839339 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 970) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C1(N(C)C)CCC1) `ZINC001281839339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001281839339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281839339 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C1(N(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 14, 14, 14, 3, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 32, 32, 32, 50, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 159 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 971) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C1(N(C)C)CCC1) `ZINC001281839339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001281839339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001281839339 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C1(N(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 12, 12, 12, 5, 1, 6, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 28, 28, 28, 48, 49, 49, 48, 48, 48, 20, 20, 20, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 28, 49, 49, 49, 49, 49, 49, 48, 48, 48, 48, 48, 48] 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]) total number of confs: 172 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001281839339 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001281839339 Building ZINC001702341864 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702341864 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/972 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001702341864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702341864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702341864 none COCc1cncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 27, 27, 27, 27, 27, 12, 7, 12, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 27, 50, 50, 50, 50, 50, 27, 27, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7, 27] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 201 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/973 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001702341864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702341864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702341864 none COCc1cncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 28, 28, 28, 28, 13, 8, 13, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 50, 50, 50, 50, 50, 28, 28, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 28] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702341864 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864 Building ZINC001702341864 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702341864 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 972) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCc1cncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001702341864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702341864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702341864 none COCc1cncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 27, 27, 27, 27, 27, 12, 7, 12, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 27, 50, 50, 50, 50, 50, 27, 27, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7, 27] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 201 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 973) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COCc1cncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001702341864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702341864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001702341864 none COCc1cncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 28, 28, 28, 28, 13, 8, 13, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 50, 50, 50, 50, 50, 28, 28, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 28] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702341864 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341864 Building ZINC001702341934 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702341934 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/974 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001702341934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702341934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001702341934 none CCN(CC)[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 29, 44, 50, 25, 29, 9, 25, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 29, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 46, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 354 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/975 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001702341934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702341934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001702341934 none CCN(CC)[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 30, 46, 50, 27, 30, 9, 27, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 30, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 46, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 326 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702341934 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934 Building ZINC001702341934 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702341934 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 974) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCN(CC)[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001702341934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702341934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001702341934 none CCN(CC)[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 29, 44, 50, 25, 29, 9, 25, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 29, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 46, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 354 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 975) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCN(CC)[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001702341934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702341934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001702341934 none CCN(CC)[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 30, 46, 50, 27, 30, 9, 27, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 30, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 46, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 326 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702341934 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341934 Building ZINC001702341939 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702341939 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/976 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001702341939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702341939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001702341939 none CCN(CC)[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 32, 46, 50, 24, 32, 10, 24, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 32, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 10, 10, 46, 46, 46, 46, 46, 46, 46] 150 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]) total number of confs: 341 number of broken/clashed sets: 138 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/977 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001702341939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702341939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001702341939 none CCN(CC)[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 34, 45, 50, 28, 34, 10, 28, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 34, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 45, 45, 45, 45, 45, 45, 45] 150 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 311 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702341939 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939 Building ZINC001702341939 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702341939 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 976) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCN(CC)[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001702341939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702341939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001702341939 none CCN(CC)[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 32, 46, 50, 24, 32, 10, 24, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 32, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 10, 10, 46, 46, 46, 46, 46, 46, 46] 150 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]) total number of confs: 341 number of broken/clashed sets: 138 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 977) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CCN(CC)[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001702341939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702341939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001702341939 none CCN(CC)[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 34, 45, 50, 28, 34, 10, 28, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 34, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 45, 45, 45, 45, 45, 45, 45] 150 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 311 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702341939 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341939 Building ZINC001702341994 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702341994 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/978 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C(C)C)cc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702341994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702341994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702341994 none Cc1nn(C(C)C)cc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 8, 8, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 50, 50, 44, 22, 10, 22, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 44, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/979 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C(C)C)cc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702341994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702341994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702341994 none Cc1nn(C(C)C)cc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 8, 8, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 48, 50, 50, 48, 23, 9, 23, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702341994 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994 Building ZINC001702341994 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702341994 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 978) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C(C)C)cc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702341994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702341994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702341994 none Cc1nn(C(C)C)cc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 8, 8, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 50, 50, 44, 22, 10, 22, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 44, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 979) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: Cc1nn(C(C)C)cc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702341994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702341994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001702341994 none Cc1nn(C(C)C)cc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 8, 8, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 48, 50, 50, 48, 23, 9, 23, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702341994 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702341994 Building ZINC001702342008 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342008 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/980 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3nccc23)C[C@@H]1O) `ZINC001702342008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702342008 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3nccc23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/981 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3nccc23)C[C@@H]1O) `ZINC001702342008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702342008 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3nccc23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342008 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008 Building ZINC001702342008 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342008 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 980) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3nccc23)C[C@@H]1O) `ZINC001702342008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702342008 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3nccc23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 981) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3nccc23)C[C@@H]1O) `ZINC001702342008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702342008 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3nccc23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342008 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342008 Building ZINC001702342041 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342041 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/982 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3ccnc23)C[C@@H]1O) `ZINC001702342041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702342041 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3ccnc23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/983 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3ccnc23)C[C@@H]1O) `ZINC001702342041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702342041 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3ccnc23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342041 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041 Building ZINC001702342041 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342041 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 982) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3ccnc23)C[C@@H]1O) `ZINC001702342041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702342041 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3ccnc23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 983) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3ccnc23)C[C@@H]1O) `ZINC001702342041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001702342041 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccn3ccnc23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342041 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342041 Building ZINC001702342158 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342158 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/984 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)Cc1ccoc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702342158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702342158 none CN(C)Cc1ccoc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 39, 39, 39, 39, 39, 16, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/985 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)Cc1ccoc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702342158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702342158 none CN(C)Cc1ccoc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 40, 40, 40, 40, 17, 10, 17, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342158 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158 Building ZINC001702342158 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342158 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 984) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)Cc1ccoc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702342158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702342158 none CN(C)Cc1ccoc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 39, 39, 39, 39, 39, 16, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 985) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CN(C)Cc1ccoc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702342158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702342158 none CN(C)Cc1ccoc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 40, 40, 40, 40, 17, 10, 17, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342158 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342158 Building ZINC001702342376 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342376 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/986 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)c1) `ZINC001702342376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702342376 none COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', '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, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 50, 50, 25, 12, 25, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/987 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)c1) `ZINC001702342376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702342376 none COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', '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, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 33, 50, 50, 19, 11, 19, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342376 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376 Building ZINC001702342376 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342376 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 986) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)c1) `ZINC001702342376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702342376 none COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', '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, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 50, 50, 25, 12, 25, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 987) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)c1) `ZINC001702342376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001702342376 none COc1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', '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, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 33, 50, 50, 19, 11, 19, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342376 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342376 Building ZINC001702342384 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342384 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/988 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C) `ZINC001702342384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702342384 none COc1cncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 11, 25, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/989 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C) `ZINC001702342384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702342384 none COc1cncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 13, 28, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 159 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342384 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384 Building ZINC001702342384 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342384 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 988) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C) `ZINC001702342384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702342384 none COc1cncc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 11, 25, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 989) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C) `ZINC001702342384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001702342384 none COc1cncc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 13, 28, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 159 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342384 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342384 Building ZINC001702342624 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342624 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/990 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc(Cl)cs2)C[C@@H]1O) `ZINC001702342624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001702342624 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc(Cl)cs2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 16, 1, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 153 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/991 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc(Cl)cs2)C[C@@H]1O) `ZINC001702342624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001702342624 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc(Cl)cs2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 16, 1, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 32, 32, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342624 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624 Building ZINC001702342624 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342624 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 990) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc(Cl)cs2)C[C@@H]1O) `ZINC001702342624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001702342624 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc(Cl)cs2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 16, 1, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 153 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 991) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc(Cl)cs2)C[C@@H]1O) `ZINC001702342624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001702342624 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc(Cl)cs2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 16, 1, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 32, 32, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342624 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342624 Building ZINC001702342771 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342771 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/992 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)cnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702342771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702342771 none COc1cc(C)cnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 29, 14, 29, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/993 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)cnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702342771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702342771 none COc1cc(C)cnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 30, 14, 30, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342771 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771 Building ZINC001702342771 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342771 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 992) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cc(C)cnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702342771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702342771 none COc1cc(C)cnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 29, 14, 29, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 993) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: COc1cc(C)cnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702342771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001702342771 none COc1cc(C)cnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 30, 14, 30, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342771 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342771 Building ZINC001702342789 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342789 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/994 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCc2ccccn2)C[C@@H]1O) `ZINC001702342789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702342789 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCc2ccccn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 18, 23, 38, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 18, 27, 27, 37, 37, 50, 50, 50, 50, 4, 4, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 229 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/995 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCc2ccccn2)C[C@@H]1O) `ZINC001702342789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702342789 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCc2ccccn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 18, 25, 38, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 18, 18, 28, 28, 37, 37, 50, 50, 50, 50, 3, 3, 9] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342789 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789 Building ZINC001702342789 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342789 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 994) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCc2ccccn2)C[C@@H]1O) `ZINC001702342789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702342789 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCc2ccccn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 18, 23, 38, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 18, 27, 27, 37, 37, 50, 50, 50, 50, 4, 4, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 229 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 995) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCc2ccccn2)C[C@@H]1O) `ZINC001702342789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001702342789 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCc2ccccn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 18, 25, 38, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 18, 18, 28, 28, 37, 37, 50, 50, 50, 50, 3, 3, 9] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342789 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342789 Building ZINC001702342857 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342857 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/996 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2(C(F)(F)F)CC2)C[C@@H]1O) `ZINC001702342857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702342857 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2(C(F)(F)F)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 204 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/997 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2(C(F)(F)F)CC2)C[C@@H]1O) `ZINC001702342857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702342857 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2(C(F)(F)F)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 31, 31, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 50, 50, 50, 50, 17, 17, 51] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 228 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342857 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857 Building ZINC001702342857 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342857 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 996) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2(C(F)(F)F)CC2)C[C@@H]1O) `ZINC001702342857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702342857 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2(C(F)(F)F)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 204 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 997) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2(C(F)(F)F)CC2)C[C@@H]1O) `ZINC001702342857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001702342857 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2(C(F)(F)F)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 31, 31, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 50, 50, 50, 50, 17, 17, 51] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 228 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342857 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342857 Building ZINC001702342860 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342860 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/998 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1[nH]cnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702342860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702342860 none CC(C)(C)c1[nH]cnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 6, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 11, 31, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 154 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/999 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1[nH]cnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702342860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702342860 none CC(C)(C)c1[nH]cnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 6, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 12, 35, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 156 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342860 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860 Building ZINC001702342860 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001702342860 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 998) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)c1[nH]cnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702342860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702342860 none CC(C)(C)c1[nH]cnc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 6, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 11, 31, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 154 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 mkdir: created directory `1' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860/1 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 1 (index: 999) grep: /scratch/xiaobo/316102/xbz-8058115.52/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: CC(C)(C)c1[nH]cnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001702342860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001702342860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001702342860 none CC(C)(C)c1[nH]cnc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 6, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 12, 35, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 156 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342860 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860/0.* 1: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860/1.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342860 Building ZINC001702342861 mkdir: created directory `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342861' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342861 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001702342861 mkdir: created directory `0' /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342861/0 /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342861 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/316102/xbz-8058115.52/working/3D/1000 `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1) `ZINC001702342861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001702342861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001702342861 none CO[C@H]1CC[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 19, 50, 10, 19, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50, 50, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 173 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342861 /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Finished preparing ZINC001702342861 Recording results /scratch/xiaobo/316102/xbz-8058115.52/working /scratch/xiaobo/316102/xbz-8058115.52 Appending to /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.* 0: /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342861/0.* Removing working files in /scratch/xiaobo/316102/xbz-8058115.52/working/building/ZINC001702342861 /scratch/xiaobo/316102/xbz-8058115.52 Compressing combined databse files /scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/316102/xbz-8058115.52/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/316102/xbz-8058115.52/working/3D/1001' removed directory: `/scratch/xiaobo/316102/xbz-8058115.52/working/3D' rmdir: removing directory, `/scratch/xiaobo/316102/xbz-8058115.52/working/building' rmdir: removing directory, `/scratch/xiaobo/316102/xbz-8058115.52/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/logs `/scratch/xiaobo/316102/xbz-8058115.52' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbz' `/scratch/xiaobo/316102/xbz-8058115.52/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbz/finished' `/scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbz/finished/xbz.db2.gz' removed `/scratch/xiaobo/316102/xbz-8058115.52/finished/xbz.db2.gz' removed directory: `/scratch/xiaobo/316102/xbz-8058115.52/finished' removed directory: `/scratch/xiaobo/316102/xbz-8058115.52'